diff --git a/lisp/doom-modules.el b/lisp/doom-modules.el
index b0c1a58d2..b2d88846a 100644
--- a/lisp/doom-modules.el
+++ b/lisp/doom-modules.el
@@ -351,9 +351,9 @@ If ENABLED-ONLY, return nil if the containing module isn't enabled."
                (and (or (null enabled-only)
                         (doom-module-p category module))
                     (cons category module))))
-            ((file-in-directory-p path doom-core-dir)
+            ((string-match (concat "^" (regexp-quote doom-core-dir)) path)
              (cons :core nil))
-            ((file-in-directory-p path doom-user-dir)
+            ((string-match (concat "^" (regexp-quote doom-user-dir)) path)
              (cons :user nil))))))
 
 (defun doom-module-load-path (&optional module-load-path)
diff --git a/lisp/lib/autoloads.el b/lisp/lib/autoloads.el
index 9dec16be5..6a31f3041 100644
--- a/lisp/lib/autoloads.el
+++ b/lisp/lib/autoloads.el
@@ -169,7 +169,6 @@ non-nil, treat FILES as pre-generated autoload files instead."
       (when (and (not (seq-find (doom-rpartial #'string-match-p file) exclude))
                  (file-readable-p file))
         (doom-log "loaddefs:scan: %s" file)
-        (setq file (file-truename file))
         (with-temp-buffer
           (if literal
               (insert-file-contents file)