Probably just incompetence on my part.
I should correct: didn't work. would probably works now. Like I said uninstall and reinstall usually gets it. The rest is probably just something I'm missing ...or derping really hard on. Probably has to do with applying the mods without obsidian's patch first being applied. Save games made before the patch are not acknowledged as even existing.
If you're curious: Stuff not triggering or inconsistently triggering like dialog and events, or lapsing between complete and incomplete.
Or light side associated things happening on dark side and vice versa.
Or stuff just not there like it wasn't installed. Even if I checked it and TSL patcher agrees with the results.