Ok, I have a weird issue that I'm experiencing. I have a setup like this (added php-style variables to provide anonymity for client and client's site):

Apache Root: C:\Project\htdocs\$client\drupal-7.22
Project Root: C:\Project\htdocs\$client\sites\$client_site.com
Breakpoint File: C:\Project\htdocs\$client\sites\$client_site.com\modules\contrib\gpt\gpt.admin.inc
output of echo __FILE__: C:\Project\htdocs\$client\sites\$client_site.com\modules\contrib\gpt\gpt.admin.inc

If I enable "Break on start" I get my index.php page as normal and I'm able to step into or over all I want. I can actually get my breakpoint in my file to trigger if I step in through the process where the debugger opens that file (yes, it opens the one that's in my project with the breakpoint). Once the file comes up, if I press F9 (continue running debbugger) it will trigger the breakpoint as expected. However, this is pretty useless as I've already manually gotten myself here anyways.

If I disable "Break on start" my project will not trigger the breakpoint when I run it, despite knowing that the conditions are right for the breakpoint to trigger.

Any ideas?

Thanks!

I'd recommend you to contact support and provide details

I have experienced the exact same problem when the editor and the debugger versions were out of sync.
Upgrading to the latest version of the debugger solved this.