The exclusions only apply for on-demand scans (see description). When otherwise using "ask", you should get one popup and then if you "allow &trust" should never see it again. Check your BeS report file under Program Data/..../Reports.
Example: Got a popup, allowed it, no more popups
Reports file says:
1/1/2011 6:18:01 AM Modification of: \REGISTRY\USER\S-1-5-21-1311629033-178814953-3054948673-1000\Software\Microsoft\Internet Explorer\Main\Save Directory
By: C:\Program Files (x86)\Online Armor\oawatch64.dll
Via: C:\Program Files (x86)\CCleaner\CCleaner64.exe
-> Action allowed
But I also get entries like
2/31/2010 5:19:29 AM Modification of: \REGISTRY\USER\S-1-5-21-1311629033-178814953-3054948673-1000\Software\Microsoft\Windows\CurrentVersion\Run\Moonrise Icon
By: C:\Program Files (x86)\Moonrise\MoonriseIcon.exe
Via: C:\Program Files (x86)\Moonrise\MoonriseIcon.exe
-> Action allowed
*
* avast! Real-time Shield Scan Report
* This file is generated automatically
*
* Started on: Friday, December 31, 2010 5:20:56 AM
*
12/31/2010 9:57:28 AM Modification of: \REGISTRY\USER\S-1-5-21-1311629033-178814953-3054948673-1000\Software\Microsoft\Windows\CurrentVersion\Run\Moonrise Icon
By: C:\Program Files (x86)\Moonrise\MoonriseIcon.exe
Via: C:\Program Files (x86)\Moonrise\MoonriseIcon.exe
-> Action allowed
*
* avast! Real-time Shield Scan Report
* This file is generated automatically
*
* Started on: Friday, December 31, 2010 9:58:50 AM
*
12/31/2010 10:00:20 AM Modification of: \REGISTRY\USER\S-1-5-21-1311629033-178814953-3054948673-1000\Software\Microsoft\Windows\CurrentVersion\Run\Moonrise Icon
By: C:\Program Files (x86)\Moonrise\MoonriseIcon.exe
Via: C:\Program Files (x86)\Moonrise\MoonriseIcon.exe
-> Action allowed
*
* avast! Real-time Shield Scan Report
* This file is generated automatically
*
* Started on: Friday, December 31, 2010 10:01:37 AM
*
12/31/2010 3:34:16 PM Modification of: \REGISTRY\USER\S-1-5-21-1311629033-178814953-3054948673-1000\Software\Microsoft\Windows\CurrentVersion\Run\Moonrise Icon
By: C:\Program Files (x86)\Moonrise\MoonriseIcon.exe
Via: C:\Program Files (x86)\Moonrise\MoonriseIcon.exe
-> Action allowed
*
which didn't generate popups, but you can't tell that from the report. Or do the trusted processes get cleared at every boot? Or Update?