Problem: when running two instances of 3ds Max the autoback of one instance will overwrite the autoback of another instance. Unfortunately that might mean that following a crash in file A there is no autoback because file B was overwriting file A each time.
Solution 1:
Make autoback smarter so the files aren't overwritten. For instance - just look at file creation and if it was created less than the autoback interval just increment the autoback file to the next number. You'll still only have your chosen number of autoback files - so you might have FileA autoback to AutoBackUp01.max, then a minute later FileB autoback to AutoBackup02.max...
Solution 2:
Just include the 3ds Max filename in the Autoback filename. For instance - instead of AutoBackup01, 02, 03 it would be MyMaxFilename_AutoBackup01, MyMaxFilename_AutoBackup02