A lot of mods there that I am unfamiliar with. However TDW's Ejecting Pilots and Thomsen's No Instant Death both overwrite the Zones.cfg file, so if you didn't do some manual editing before enabling you lost any changes made to that file by Thomsen's mod that were not also included in TDW's version of it.
Also I'm pretty sure that Renown Replacement and Additional Ammo both overwrite the basic.cfg so the same caveat applies. I doubt that this has anything to do with the issues you're having though.
Can't say I know one way or the other about Zones.cfg, I haven't played around with that file myself (yet).
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