marinelover28540:

The command windows are most likely executing deletes of files that were in use when Spybot first attempted to delete them.

If Spybot encounters a file that can not be deleted it adds a "RunOnce" startup entry so that during the next system startup another attempt is made to delete the file. The entries added for the execution of the delete commands at system startup would look similar to the following:

Code:
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnce]
"SpybotDeletingxnnn"="command.com /c del \"*** filename ***""
"SpybotDeletingxnnn"="cmd.exe /c del \"*** filename ***""