Definitely a Denise issue, the mouse counters live there.
If you've ruled out the chip itself it may very well be the 'wobbly' connection. Try holding Denise firmly but carefully down while firing up the system and trying the mouse.
Don't know what the Indivision's socket looks like but you can probably try plugging a quality socket under Denise, it'll make a firmer connection. All photos I can find show the Indy with a nice socket, possibly yours got damaged somehow.
