I have found and confirmed this a couple of times in my experiences that Mods with scrips that are packed into a .BSA and has a "compressed" flag, will causes issues with scripts sometimes not functioning properly. The general scripts that somehow have I had issues with are mods with the MCM, and mods that have scripts that work on loading a save.

I guess this is really an issue which is why a lot of mods prefer to have their scripts directory separate and loose from an archive.

If anyone can also confirm this please reply below.

Uncompressed archives though haven't caused this issue for me as far as my experience with this goes..