The program that I'm using is foobar2000 v1.3.15. As for vgmstream, version r1050-1102-g95d9a7f5 (the latest version by the time of writing this comment).
I tried your settings with those files and they sound the same to me. I don't really understand your issue, what do you mean with "can't loop properly or loops quickly"?
Even if the duration is slightly different between files it's basically inaudible.