Sorry guys I almost no knowledge about Vista new security layer.
I've read all related topics and have few clues.
But there is no easy way to get a definite idea.
Also there is no easy way to guess what's going on reading the generic user feedback as it looks like tha some info are missing or unasked.
IIRC the related issues I know are:
1. Updates are not acknowledged.
2. CFP reports the wrong version in the about box.
3. Some files are not updated.
So the only thing I can do ATM is to post the few clues I have.
My clues are based on the following assumptions:
- Admins on Vista usually run with limited privileges. When an action or a software require full admin privileges an UAC elevation prompt is displayed.
- Write Access to program files folder or important registry entries require full admin privileges
- When a low privilege process(application) attempt to write in an area that require full privileges those actions are redirected to a virtual area and are stored in the user profile folder
- cfpupdat.exe check cfpver.dat to find out the version. if cfpver.dat is deleted will always find a new version
Those who get the wrong version maybe have a cfpver.dat in the virtualized comodo folder.
Those whose files cannot updated got the update totally denied or redirected to virtualized comodo folder.
Those who posted their UAC settings so far should get an UAC elevation prompt on every update so they should have no issues but this is not the case

I wonder what happens if cfpupdat.exe is run as administrator using the right-click context menu.
The appdata folder is a hidden folder under the user profile
it contains 3 other folders: Local LocalLow and Roaming
redirected file writes should be available into C:\Users\User_name\AppData\Local\VirtualStore\Program Files\ MyApp folder
Further reading:
Common file and registry virtualization issues in Windows Vista