It sounds like you have swapped everything around except for the wiring, meaning after you made the changeover. So if you have used the same wiring on the Z axis each time you changed a part ( like swapped drives, motor ect,ect) then try different wiring harness for the Z axis.
Also try different ports on the BOB, like run the Z axis where you had the X or Y hooked to the BOB (both to and from the BOB).
And just because the problem showed itself when you made a change doesnt mean something else didnt happen so stay open minded about it.
What about the connections, or ports them self between the BOB and the computor?
If you do go as far as changing BOB's again I would suggest the PMDX products. CNC4PC does seem to have a board here and there that leave the shop with a problem. WIth that said they are good about backing there products. Also I dont know which product doesnt work good with others but it seems I read here and there about X BOB didnt work well with X setup in the CNC4PC line.
Problems like this can be hard to track down sometimes. Just dont let it get you flustered and try to work systematically and keep notes about what you try.
And like I said earlier be open minded. A machanical problem could even just happened to start at the same time. Have you checked the pully and belts on the Z axis? Could the wire for the encoder have a intermiting break in it? Does the Axis try to bind at any one point? There is a ton of little things that could be causing the problem so give everything thought. Wires along being routed differently may show a open or shorted curcuit just by being routed in a different dirrection. Might have been good before but with different stress from different routing could show the problem up.
Good luck, Jess
GOD Bless, and prayers for all.