Well, I think the problem doesn't have anything to do with the number of files. My guess is that one of the files is "stored" (i.e. archived without any compression) in the .RAR archive. This way, avast! scanner finds it both during the decompression of the archive, and also during the scanning of the "outer" file (because the stored file is clearly visible there - it would be detected even with archives turned off).
When found inside of the archive, only the corresponding file is deleted; when detected in the "envelope", however, the whole archive is deleted.
I'm just trying to improve the behavior somehow... but I'm afraid the problem is not 100% solvable. Changing the behavior one way will make another problem appear elsewhere. Regarding the actions on archives, there always will be situations when it doesn't work right, I'm afraid.