This is a long shot, but in your PHP can you check whether you’re using the shorthand PHP opening tag (ie, <% rather than <%php) - I noticed after the upgrade to 1.4.1 that’s now been disabled by default and will give a Error 500 if you try and use it.
If that’s the case, either enable the shorthand in your PHP config, or go through your PHP scripts and make sure you’re not using <%
Pete