diff --git a/.github/workflows/codeowner-review-request.yml b/.github/workflows/codeowner-review-request.yml
index 121619e049..ab3377365d 100644
--- a/.github/workflows/codeowner-review-request.yml
+++ b/.github/workflows/codeowner-review-request.yml
@@ -182,11 +182,14 @@ jobs:
               });
 
               // Check for previous comments from this workflow to avoid duplicate pings
-              const { data: comments } = await github.rest.issues.listComments({
-                owner,
-                repo,
-                issue_number: pr_number
-              });
+              const comments = await github.paginate(
+                github.rest.issues.listComments,
+                {
+                  owner,
+                  repo,
+                  issue_number: pr_number
+                }
+              );
 
               const previouslyPingedUsers = new Set();
               const previouslyPingedTeams = new Set();
@@ -194,7 +197,6 @@ jobs:
               // Look for comments from github-actions bot that contain our bot marker
               const workflowComments = comments.filter(comment =>
                 comment.user.type === 'Bot' &&
-                comment.user.login === 'github-actions[bot]' &&
                 comment.body.includes(BOT_COMMENT_MARKER)
               );
 
diff --git a/.github/workflows/external-component-bot.yml b/.github/workflows/external-component-bot.yml
index 5f5bc703ad..29103e8eee 100644
--- a/.github/workflows/external-component-bot.yml
+++ b/.github/workflows/external-component-bot.yml
@@ -61,7 +61,8 @@ jobs:
             }
 
             async function createComment(octokit, owner, repo, prNumber, esphomeChanges, componentChanges) {
-                const commentMarker = "<!-- This comment was generated automatically by a GitHub workflow. -->";
+                const commentMarker = "<!-- This comment was generated automatically by the external-component-bot workflow. -->";
+                const legacyCommentMarker = "<!-- This comment was generated automatically by a GitHub workflow. -->";
                 let commentBody;
                 if (esphomeChanges.length === 1) {
                     commentBody = generateExternalComponentInstructions(prNumber, componentChanges, owner, repo);
@@ -71,14 +72,23 @@ jobs:
                 commentBody += `\n\n---\n(Added by the PR bot)\n\n${commentMarker}`;
 
                 // Check for existing bot comment
-                const comments = await github.rest.issues.listComments({
-                    owner: owner,
-                    repo: repo,
-                    issue_number: prNumber,
-                });
+                const comments = await github.paginate(
+                    github.rest.issues.listComments,
+                    {
+                        owner: owner,
+                        repo: repo,
+                        issue_number: prNumber,
+                        per_page: 100,
+                    }
+                );
 
-                const botComment = comments.data.find(comment =>
-                    comment.body.includes(commentMarker)
+                const sorted = comments.sort((a, b) => new Date(b.updated_at) - new Date(a.updated_at));
+
+                const botComment = sorted.find(comment =>
+                    (
+                      comment.body.includes(commentMarker) ||
+                      comment.body.includes(legacyCommentMarker)
+                    ) && comment.user.type === "Bot"
                 );
 
                 if (botComment && botComment.body === commentBody) {
diff --git a/.github/workflows/issue-codeowner-notify.yml b/.github/workflows/issue-codeowner-notify.yml
index 27976a7952..3639d346f5 100644
--- a/.github/workflows/issue-codeowner-notify.yml
+++ b/.github/workflows/issue-codeowner-notify.yml
@@ -29,6 +29,9 @@ jobs:
 
             console.log(`Processing issue #${issue_number} with label: ${labelName}`);
 
+            // Hidden marker to identify bot comments from this workflow
+            const BOT_COMMENT_MARKER = '<!-- issue-codeowner-notify-bot -->';
+
             // Extract component name from label
             const componentName = labelName.replace('component: ', '');
             console.log(`Component: ${componentName}`);
@@ -93,11 +96,14 @@ jobs:
               );
 
               // Check for previous comments from this workflow to avoid duplicate pings
-              const { data: comments } = await github.rest.issues.listComments({
-                owner,
-                repo,
-                issue_number: issue_number
-              });
+              const comments = await github.paginate(
+                github.rest.issues.listComments,
+                {
+                  owner,
+                  repo,
+                  issue_number: issue_number
+                }
+              );
 
               const previouslyPingedUsers = new Set();
               const previouslyPingedTeams = new Set();
@@ -105,9 +111,8 @@ jobs:
               // Look for comments from github-actions bot that contain codeowner pings for this component
               const workflowComments = comments.filter(comment =>
                 comment.user.type === 'Bot' &&
-                comment.user.login === 'github-actions[bot]' &&
-                comment.body.includes(`component: ${componentName}`) &&
-                comment.body.includes("you've been identified as a codeowner")
+                comment.body.includes(BOT_COMMENT_MARKER) &&
+                comment.body.includes(`component: ${componentName}`)
               );
 
               // Extract previously mentioned users and teams from workflow comments
@@ -140,7 +145,7 @@ jobs:
 
               // Create comment body
               const mentionString = allMentions.join(', ');
-              const commentBody = `👋 Hey ${mentionString}!\n\nThis issue has been labeled with \`component: ${componentName}\` and you've been identified as a codeowner of this component. Please take a look when you have a chance!\n\nThanks for maintaining this component! 🙏`;
+              const commentBody = `${BOT_COMMENT_MARKER}\n👋 Hey ${mentionString}!\n\nThis issue has been labeled with \`component: ${componentName}\` and you've been identified as a codeowner of this component. Please take a look when you have a chance!\n\nThanks for maintaining this component! 🙏`;
 
               // Post comment
               await github.rest.issues.createComment({
diff --git a/esphome/core/application.cpp b/esphome/core/application.cpp
index 873f342277..4fedd36120 100644
--- a/esphome/core/application.cpp
+++ b/esphome/core/application.cpp
@@ -55,6 +55,9 @@ void Application::setup() {
     return a->get_actual_setup_priority() > b->get_actual_setup_priority();
   });
 
+  // Initialize looping_components_ early so enable_pending_loops_() works during setup
+  this->calculate_looping_components_();
+
   for (uint32_t i = 0; i < this->components_.size(); i++) {
     Component *component = this->components_[i];
 
@@ -97,7 +100,6 @@ void Application::setup() {
   clear_setup_priority_overrides();
 
   this->schedule_dump_config();
-  this->calculate_looping_components_();
 }
 void Application::loop() {
   uint8_t new_app_state = 0;
@@ -269,24 +271,16 @@ void Application::calculate_looping_components_() {
   // Pre-reserve vector to avoid reallocations
   this->looping_components_.reserve(total_looping);
 
-  // First add all active components
+  // Add all components with loop override
+  // When called at start of setup, all components are in CONSTRUCTION state
+  // so none will be LOOP_DONE yet - they'll all go in the active section
   for (auto *obj : this->components_) {
-    if (obj->has_overridden_loop() &&
-        (obj->get_component_state() & COMPONENT_STATE_MASK) != COMPONENT_STATE_LOOP_DONE) {
+    if (obj->has_overridden_loop()) {
       this->looping_components_.push_back(obj);
     }
   }
 
   this->looping_components_active_end_ = this->looping_components_.size();
-
-  // Then add all inactive (LOOP_DONE) components
-  // This handles components that called disable_loop() during setup, before this method runs
-  for (auto *obj : this->components_) {
-    if (obj->has_overridden_loop() &&
-        (obj->get_component_state() & COMPONENT_STATE_MASK) == COMPONENT_STATE_LOOP_DONE) {
-      this->looping_components_.push_back(obj);
-    }
-  }
 }
 
 void Application::disable_component_loop_(Component *component) {
diff --git a/esphome/core/lock_free_queue.h b/esphome/core/lock_free_queue.h
index de07b0ebba..68e2825d09 100644
--- a/esphome/core/lock_free_queue.h
+++ b/esphome/core/lock_free_queue.h
@@ -29,7 +29,7 @@ namespace esphome {
 // Base lock-free queue without task notification
 template<class T, uint8_t SIZE> class LockFreeQueue {
  public:
-  LockFreeQueue() : head_(0), tail_(0), dropped_count_(0) {}
+  LockFreeQueue() : dropped_count_(0), head_(0), tail_(0) {}
 
   bool push(T *element) {
     bool was_empty;