Firstly avast doesn't delete autonomously either on boot or otherwise, it alerts to infection and you the user choose the action to be taken. I presume avast isn't alerting on this program (or you would have mentioned it) ?
Files that can't be scanned are just that, not an indication they are suspicious/infected, just unable to be scanned.
However, you can make selections on what to do with these files after the scan, you should take no action at all, close the window. So did you select an action ?
Many programs (usually security based ones) password protect their files for legitimate reasons such as AdAware and Spybot Search & Destroy, there are others (and avast doesn't know the password or have any way of using it even if it did know it).
When you run scans with the above programs and you delete harmful entries that they detect, a copy is kept (in quarantine/restore/backup) in case you need to reverse what you did. These are usually password protected, you should do some housekeeping and delete old backup/recovery/quarantine entries (older than two weeks or so), this will reduce the numbers of files that can't be scanned.
By examining 1) the reason given by avast! for not being able to scan the files, 2) the location of the files, you can get an idea of what program they relate to. You may need to expand the column headings to see all the text. If you can give some examples of those file names, the locations and reason given why it can't be scanned might help us further ?