Perhaps I can be of some assistance, given that I'm an audio DSP software coder.
Although I've been away from this project for a long time, as you may have heard I'm coming back and working on getting caught up.
Writing C/C++ code for resampling audio on-the-fly (in realtime) is indeed one of my skills. What I'm not too familiar with, though, is SDL2 and exactly how it handles sound.
I was working on upgrading my ancient Linux distro to a current version with all packages, but given that this issue was reported on Windows, I suppose I could get a copy of the source and set it up on one of my Windows machines, most likely by sometime later today.
I could use some help in being directed to what parts of UFO AI (which source code files) are used to interact with SDL2, and then I might be willing to help troubleshoot the issue. (And if it is with SDL2 and not UFO AI, I could then send a patch to the SDL devs.)
BTW, my Windows machines have Windows 7 x64, Windows 7 x32, and one has Windows 8.1. I also have some special "pro-sumer" (professional audio engineering-grade, intended for high-end recording studio) level soundcards as well as basic built-in ones in the Windows machines, so I could definitely find out if it is a soundcard issue or not.