Upon upgrading to PHP 4.1.2, all calls which use the file_exists() function to verify files within a non-existent sub-directory, are generating a stat warning (which was not the case in 4.0.6). 

Example code:
if (file_exists($dir.'/filename.ext')) { 
  FOO;
}

If $dir doesn't exist, the following warning is generated:

Warning: stat failed for dir/filename.exe (errno=20 - Not a directory) in script.php on line n.

This is easily silenced by calling @file_exists instead, but it doesn't seem like the desired behavior.