diff --git a/src/Psalm/Internal/Analyzer/ProjectAnalyzer.php b/src/Psalm/Internal/Analyzer/ProjectAnalyzer.php
index d0d1766750e..d2531d85af4 100644
--- a/src/Psalm/Internal/Analyzer/ProjectAnalyzer.php
+++ b/src/Psalm/Internal/Analyzer/ProjectAnalyzer.php
@@ -264,6 +264,8 @@ public function __construct(
         int $threads = 1,
         ?Progress $progress = null
     ) {
+        self::$instance = $this;
+
         if ($progress === null) {
             $progress = new VoidProgress();
         }
@@ -289,6 +291,7 @@ public function __construct(
         $this->stdout_report_options = $stdout_report_options;
         $this->generated_report_options = $generated_report_options;
 
+        $this->config->initializePlugins($this);
         $file_extensions = $this->config->getFileExtensions();
 
         foreach ($this->config->getProjectDirectories() as $dir_name) {
@@ -314,8 +317,6 @@ public function __construct(
         foreach ($this->config->getProjectFiles() as $file_path) {
             $this->addProjectFile($file_path);
         }
-
-        self::$instance = $this;
     }
 
     private function clearCacheDirectoryIfConfigOrComposerLockfileChanged() : void
@@ -435,7 +436,7 @@ public function server(?string $address = '127.0.0.1:12345', bool $socket_server
             }
         }
 
-        $this->config->initializePlugins($this);
+        #$this->config->initializePlugins($this);
 
         foreach ($this->config->getProjectDirectories() as $dir_name) {
             $this->checkDirWithConfig($dir_name, $this->config);
@@ -589,7 +590,7 @@ public function check(string $base_dir, bool $is_diff = false): void
             $this->codebase->scanner->addFilesToDeepScan($this->project_files);
             $this->codebase->analyzer->addFilesToAnalyze($this->project_files);
 
-            $this->config->initializePlugins($this);
+            #$this->config->initializePlugins($this);
 
             $this->codebase->scanFiles($this->threads);
 
@@ -612,7 +613,7 @@ public function check(string $base_dir, bool $is_diff = false): void
 
                     $this->checkDiffFilesWithConfig($this->config, $file_list);
 
-                    $this->config->initializePlugins($this);
+                    #$this->config->initializePlugins($this);
 
                     $this->codebase->scanFiles($this->threads);
                 } else {
@@ -994,7 +995,7 @@ public function checkDir(string $dir_name): void
 
         $this->progress->startScanningFiles();
 
-        $this->config->initializePlugins($this);
+        #$this->config->initializePlugins($this);
 
         $this->codebase->scanFiles($this->threads);
 
@@ -1125,7 +1126,7 @@ public function checkFile(string $file_path): void
 
         $this->progress->startScanningFiles();
 
-        $this->config->initializePlugins($this);
+        #$this->config->initializePlugins($this);
 
         $this->codebase->scanFiles($this->threads);
 
@@ -1166,8 +1167,7 @@ public function checkPaths(array $paths_to_check): void
 
         $this->progress->startScanningFiles();
 
-        $this->config->initializePlugins($this);
-
+        #$this->config->initializePlugins($this);
 
         $this->codebase->scanFiles($this->threads);
 
diff --git a/src/Psalm/PluginRegistrationSocket.php b/src/Psalm/PluginRegistrationSocket.php
index ea1576ef4e6..db4e8ac0384 100644
--- a/src/Psalm/PluginRegistrationSocket.php
+++ b/src/Psalm/PluginRegistrationSocket.php
@@ -204,7 +204,9 @@ public function getAdditionalFileExtensions(): array
      */
     private function addFileExtension(string $fileExtension): void
     {
-        if (!in_array($fileExtension, $this->config->getFileExtensions(), true)) {
+        if (!in_array($fileExtension, $this->additionalFileExtensions, true)
+            && !in_array($fileExtension, $this->config->getFileExtensions(), true)
+        ) {
             $this->additionalFileExtensions[] = $fileExtension;
         }
     }