They offer Ghost pickups to match a lot of bridges, but I don't know if the 89 is one of them.

There is someone who has posted reviews of the Tyler Variax on some of the big chain stores sites stating that they changed them out for the Graphtech Ghost pickups as part of a transplant.  "They have a clearer tone that you can't achieve otherwise.  (Graph Tech pickups:  blue is the positive wire)  "

They go on to state that you have to adjust/lower the output in Workbench because they will overload the input and distort if you don't.

The circuit board under the bridge of the JTV-89 has positive and negative solder contacts for each string, even though the Baggs doesn't require them.  So the contacts (grounds for the blue wires) are there if you need them.

I would guess this might be where your problem is, these solder contacts.  You would first have to pull out the push-in connector from the pickups on the main cuircut board in the back of the guitar to allow the bridge and the small cuircut board hidden under it to be removed from the front of the guitar.  There is a little silicon covering each pickup wire on this small circuit board from under the bridge.  Remove the silicon from the contact corresponding to the string that is intermitten, resolder the connection, dab on fresh silicon and try it.