I took my Fliptronics II board out to try it in my WH20 (where I ended up having a bad transistor) and when I put it back in TZ the flippers do not now work in play, but when I go to flipper test in the diagnostics they do.
When I go to switch test and press on the flipper buttons, they both do not register on the matrix.
If I close the flippers manually the EOS switches register.
I swapped in the (repaired) Fliptronics board from WH20 and no luck. I also swapped in an opto board and that made no difference either.
So it doesn't seem to be a flipper opto switch board or a Fliptronics board issue.
Any ideas where to go from here?

Thanks, rechecked them all and they are ok.

It's not the board as I swapped the WH2O board in and same problem.

Yes that is right, the cabinet switches don't register. Physically they are fine, and I also swapped a confirmed working opto board in.
So I am guessing it's the connection from the flipper opto boards to the head that's the problem (maybe when I pulled the Fliptronics board out something happpened) but I'm unsure how to test for a solution.

That was it thanks Coyote, I pushed the orange wire in on connector J905 and it came up on switch test - all good now. Thanks for narrowing it down for me.