I've uploaded an alternate verison of NeoLemmix V1.43n-F. This doesn't contain any new features or changes in mechanics from V1.43n-F; the only difference is that it disables windowed mode, and removes some of the behind-the-scenes code to support it. Hence, it is labelled V1.43n-F-alt, rather than V1.43n-G.
The reason for this is that the code that enables windowed mode can cause issues on WINE, and with certain recording software. This is not guaranteed to fix issues, but you can try it if you're having such problems. On Windows, in the absence of recording software, it makes no difference.
I have tried with Ubuntu and the LXDE desktop, and it does not help for me. Another user tried on Ubuntu with the Unity desktop, and said it fixed the problems they were having. Yet another user who uses Debian (I'm not sure what desktop) and an older version of WINE never had problems in the first place.
In regards to recording software, I haven't had any feedback as to what it does or doesn't improve. Open Broadcaster Software does not have issues with NeoLemmix in the first place, provided Screen Capture mode is used. XSplit seems to have issues, according to one streamer; I have no feedback yet as to whether or not this version helps. Another piece of software, which I can't remember the name of (but might've been a CyberLink product) also doesn't appear to have issues in the first place.
So - if you're having any such issues - feel free to try it. I can't promise it will fix anything, but it can't hurt to try.
The normal version of course still remains available, and I recommend you use the normal version unless you're specifically having any problems of those natures.
I'll continue to see if I can improve the de-windowing in this version, since most people say that V1.37n (the last version without windowed mode) or EXE-based standalone players (also lacking windowed mode) didn't have these problems.