the program has been deleting temp files when you perform a full scan. it's not supposed to do this. I can't remember for sure, but it may also delete internet explorer temporary files as well. this is consistent behavior.
why not delete temp files?
- many programmers who write application installers write them (including some big names) so that extraction by default goes to the temp directory.. if you delete the extracted installer, your program may not uninstall, or may not even function anymore (I have seen this happen after a cleanup with some programs), since sometimes part of the program is installed in the temp directory too. I don't recommend this sort of practice to programmers, but it is done nonetheless, probably because it's not protected by windows and supposedly always works. not anymore with recent antivirus and registry/pc cleaner/pc optimization programs.
- Microsoft Word and Office leaves ~ (tilde)-named temp files around, but in the directory your file is located in. sometimes, it leaves the temp file behind for no apparent reason and it's just talking up needless space I guess. these should be left alone probably, unless Word has it open. it might be locked or it might not. it may be a shortcut, in which case deleting it deletes the original file. be careful. that would require testing.
- other programs may be using the temp directory at that time, and may have files in use. usually those files are locked. but they MAY be opened with file share read and write permissions. if this is the case, and it is deleted, the running program could mess up.
- it's not necessary to speed up a machine.
when to do this is you must: during reboot.
many times, just having too many files in 1 dir (like 1000 of them) can slow down the machine just trying to access the dir. the temp directory is like this, but like I said it's best left alone, like /var/tmp on *nix. you don't mess with it unless you are creating a file you are going to work with yourself, and you make sure you delete it when you are done.
I just want you to be a little more careful about this practice, not doing it would be best.