Okay, I don't know, what you mean by "backup file". But what you describe, seems to be a bug. This has been reported some time ago and only effects Windows systems. See http://ez.no/community/bug_reports/new_binary_files_sometimes_overwrite_existing_binary_files
Also, your 3.3 version is quite old, i suggest, that you update to the latest 3.3 or 3.4 version. The bug is reported to be fixed since 3.3.6
BTW: I'm using 3.3-3, too, on a Solaris system, and did not have that bug with approx. 1000 files uploaded