There may be more reasons why the files were not scanned (they can be too small to contain a virus, for example) - but usually the reason is that during the runtime of the operating system, some files are simply not accessible - e.g. the swap file. There's no reason to worry about this one - it's not infectable anyway.
If you could post the content of the report file (i.e. the list of the files that were not scanned, together with what avast! announced exactly), we could tell a little more...