The inconsistencies of the results when scanning such a multi-virus archive may be caused by so called "paranoid mode". When avast! finds the first virus (which is rather a rare event on an ordinary user computer), it switches to a paranoid mode, scanning all files, whole files, etc.
As for the problem with the deleting of the file... I did quite a lot of debugging today and I think I found a bad bug that may cause strange behavior. You may try the following (however weird it seems): go to the program settings and change to the "Report file" page. There, turn off every option that can be turned off there (even the disabled ones - i.e. first, make sure the report file creation is on, uncheck the options and turn the report file creation off again. Does it help to delete the infected 646.exe file?