I definitely see that SGP is creating new files for duplicates and renaming them correctly:
[6/5/2016 2:02:19 PM] [DEBUG] [Sequence Thread] Created full file name (file does not exist): C:\Users\SJAA\Pictures\SGP\M51\Bias\M51_0sec_2x2__frame1.fit
[6/5/2016 2:52:47 PM] [DEBUG] [Sequence Thread] Created full file name: C:\Users\SJAA\Pictures\SGP\M51\Bias\M51_0sec_2x2__frame1-1.fit
[6/5/2016 2:57:46 PM] [DEBUG] [Sequence Thread] Created full file name: C:\Users\SJAA\Pictures\SGP\M51\Bias\M51_0sec_2x2__frame1-2.fit
[6/5/2016 2:59:29 PM] [DEBUG] [Sequence Thread] Created full file name: C:\Users\SJAA\Pictures\SGP\M51\Bias\M51_0sec_2x2__frame1-3.fit
[6/5/2016 3:00:58 PM] [DEBUG] [Sequence Thread] Created full file name: C:\Users\SJAA\Pictures\SGP\M51\Bias\M51_0sec_2x2__frame1-4.fit
I'm not sure how you "sorted by gain" but it appears that SGP did NOT overwrite any files. Maybe just not how you're expecting to find them?
Thanks,
Jared