I didn't make any changes to the permission system, permissions are enforced based on pageid and module id not on page name.
However, I cannot be expected to support scenarios where my implementation is replaced by third party implementations. I do not use that url rewrite module you are using and I do not test it so I would never know if it worked or got broken by a change I made.
I recommend you step through the code and see what is happening. I would set a breakpoint at line 69 in SiteModuleControl where is Editable is determined.
Sorry I can't be more help.