No, I don't think we need fakepatch with 1.6. UFP, however, may have problems with 1.6. I haven't kept up to speed but I seem to remember a discussion where it was causing problems with 1.5 and needed to be updated?
Make sure you followed the update procedure properly, and if you use FWE rest 9 days instead of 4.
That said, there is a 'ever increasing' spawns bug I need to fix at the Citadel, and this could be it. This is a single scripted location though, so if it's happening anywhere you haven't done the upgrade process.
Good to hear
http://img78.imageshack.us/i/screenshot0p.png/
Did you follow the update procedure, detailed at the top of the first post of this thread, to the letter?
MMM doesn't alter any followers or any quest-related NPCs (with a few exceptions, like Hoss to give him some backup if Increased Spawns is enabled). It also doesn't alter any AI packages -- it adds its own new unique ones.
Yes it could be FOOK -- don't use the 'Enemy Rebalanced' plugin if you have it. This unnecessarily edits hundreds of NPCs, and prevents Broken Steel quest from starting once it was installed as Lyons and his script are (unnecessarily) altered. While FOOK has many awesome qualities, keep in mind it's a very dirty mod. Lots of references that shouldn't have been touched, deleted references that can cause CTDs, world edits that don't need to be there, and corrupted level lists. I cleaned the early versions for Linkesauge but his... modding habits kept adding more errors (even though I gave some detailed guidelines on what to avoid doing). Someone else took over cleaning duties and FOOK 2.0 should be much better, but be aware 1.6 has lots of issues.