Well, the master "how to fix this" post is at B3, whicjh is down, so to cut to the chase (if you don't understand, just ask in this thread).
To use Walking Speeds best, install it at the end of your install. (It still has some wierd consequences on Polymorph Self spells and Slow, but Haste, Grease, etc. will work fine. I always play with it when I am not testing something.)
Once you have uninstalled it, the Save still has all of the characters you have met saved in the old state (and any areas you have visited asr saved with the changes as well). You can't do much about areas you have visited that doesn't involve some pretty heavy (and silly) surgery, but you can fix your joined NPC's easily.
Open ShadowKeeper, load the savegame you wnat to fix, and look under the tab "affects". There you will see a line that says something like
0x00B0 -3
Clear that line from each one of the characters (check them all).
Voila - default BG2 walking speeds are restored.
CamDawg and SimDing0 are looking into repairing this behavior and moving the component to the BG2 Tweak Pack' s first non-beta version.