Where are the Microsoft application compatibility update settings stored on a Windows XP, Windows Vista, and Windows 7 computer?

Microsoft periodically release application compatibility updates (e.g. KB929427), where they list the shims that should be applied to a program in order to workaround known bugs in the software. Where are these app compat flags stored, and how can i see what shims are being applied?

i have a feeling that a recent app compat update included a flag to force a particular piece of software, that we use, to require administrator. Because the task is scheduled to run nightly, and the running user does not have administrative privelages, the task is failing to start.

The application is requiring to be elevated. It has the UAC shield overlay. The application has no RT_MANIFEST resource, and the compatibility option Run this program as administrator is disabled (per-user and all users). So all that's left is some secret global setting.

i know user-specified compat flags are stored in:

HKEY_LOCAL_MACHINE
   \SOFTWARE
     \Microsoft
       \Windows NT
         \CurrentVersion
           \AppCompatFlags
             \Layers