I am having a similiar problem ..
all the menu's work on the home page.. however when I go into select threads (random threads) they stop working (navbar menu's , thread tools etc.)
This started after I did my upgrade from 3.0.7 to 3.5.4.. any ideas?!?!
checked my footer template and it looks ok?!?!
www.trackshare.com
I was doing some searching on this and it seems to be related to the navbar.. I reverted mine to test and it fixed this issue.. Does anyone know exactly what would cause this though?!? I don;t want to have to reconfigure my navbar as I forgot most of the stuff I did to it to get it to look like it does now!