I also have had a problem with exclusions.
I placed an exclusion for a directory containing 'Malware' in the [Settings] Master Exclusion List (per documentation). Avast 5.0.418 was very efficient at moving it to the Chest over every time I dropped the 'Malware' in the directory over a period of a half hour (keep trying in case there was 'lag' in the exclusions list updating). Only by placing an entry for the directory in the [File System Shield] Exclusions was I able to get Avast to exclude the file.
I hope this bug is addressed so the [Settings] Master Exclusions work again. I also recommend some simple method of placing a file or class into the exclusion list. One place would be to add on option to exclude the file when restoring it from the Virus Chest. The option could be to exclude just the file or the class (i.e., Malware:Gen Type a3). I've changed the [Action] to 'ask' and see what happens.
I know this isn't a thread for 'features', but it would be nice to have all the events (Virus or trojan found, moved to chest, updated defs, etc.) available in the system event log.
I like Avast and V5 shows a nice improvements throughout.