I'm having some problems getting XNT to work as well. I've got the latest Xenonauts and the .34 CE (well, .34.1 as of today), but if I toss in XNT and the .exe files, the mod selection gets.. Weird, and it seems to want to activate all of the mods ever, so when I first opened up the game everything was in French! Somewhat problematic for me as I don't speak the language. Went in and deleted all of the FR mods, everything seemed fine then though once I got into combat the game would hang on alien turns, indefinitely, nothing I could do to fix that. So I switched back to the default .exe set and now the game just crashes whenever I try to place my first base. Any advice? I tried removing some of the mods that are on by default but that fixed nothing.
I really want to give XNT a try because it looks amazing, if a bit dated.
I tried XDivision but I absolutely hated how from day one various types of aliens were pretty much invulnerable to different damage types except the one and only one that is effective against them.