When you uninstalled all the mods, did you start a new game or are you still using a save that had those mods in it?
I have a real boinked game that I have 2 heavily scripted followers and a lot of scripted mods. Installing either of the last 2 versions of HDT-PE the followers spaz when going from an interior to exterior cell or exterior to interior one.
Strangely, I have yet to get them to spaz when fast traveling. I've noticed that UFO, which I use, "redresses" the followers on the first 2 set of cell changes (see green aura on follower) and does not "redress" them on a fast travel.
So, my guess is that it may come down to what UFO is doing to the followers. My PC hasn't yet had a problem. I believe you had AFT installed.
Active scripts do not go away on a mod uninstall. Backup your saves and try and use SaveTool (on the Nexus site) on one of you minimum saves and see if that might clean that save up a bit.