avast! doesn't skip the files "randomly", of course - it has a reason for not scanning them. For example, if the files are too small to contain a virus (e.g. 5 bytes), it's not necessary to scan them. When avast! is set to scan executable files only, and the file is not identified as executable, it will not be scanned either.
So, I think the question should stand - how did you perform the scan? What were the settings/sensitivity you specified?