Twice in the past two days I've been working in a large WAP which use IIS, and when I compile and view in the browser I received a permissions error, that ASP.NET does not have permissions to a file.  The first time it was to an aspx that had been previsoul working.  I look at the file's permissions and sure enough IIS_WPG no longer had any permissions to the file...and a lot of other aspx files in the project had also lost their permissions.   I reset the permissions for all the files by setting at the folder level and propagating them to all child objects.   Everything work fine until a day later, while working in the WAP again the same thing happened, only this time the permission error occured on the web.config.  Sure enough IIS_WPG permissions were lost on a lot of files in the project and I had to reset them.
The WAP is also source safed so files have been getting checked in/out.  I don't know if this is an issue related to WAP,  VSS,  just my win2k3 machine, VS2005 in general or some combination of  these  (though WAP may not be the cause, since it's in a WAP I thought I might as well start out in this forum).  In the months of beta testing WAP, even on the same project, I never saw this error until yesterday (though I've been doing some major work in the project this week).