Below patch removes the folder separator of the temporary-file-directory, works fine in my environment.
diff --git a/lisp/progmodes/flymake-proc.el b/lisp/progmodes/flymake-proc.el
index 7cdbb266fe..f0b979185e 100644
@@ -886,7 +886,7 @@ can also be executed interactively independently of
(defun flymake-proc--delete-temp-directory (dir-name)
"Attempt to delete temp dir created by `flymake-proc-create-temp-with-folder-structure', do not fail on error."
- (let* ((temp-dir temporary-file-directory)
+ (let* ((temp-dir (directory-file-name temporary-file-directory))
(suffix (substring dir-name (1+ (length temp-dir)))))
(while (> (length suffix) 0)