It could be that the Roto target isn't coming to rest in the right place. It has wipers and contacts like any stepper. It's important that the wipers stop directly over the contacts and not in between. HowardR recently pointed to an article about adjusting Roto units in this post:

https://pinside.com/pinball/forum/topic/64-ship-mates-rototarget-not-resetting#post-4833180

/Mark

These kind of oddball experiences can drive you nuts. I'd check the wire loom to see if it is rubbing an edge somewhere. More than once I have had some loss of wiring insulation where the loom may ride against a metal edge or back of the playfield. You raise the playfield and the wires move just enough to eliminate the problem. Setting it back down and wear among a couple wires lines up and causes a short. Of course it could be something else entirely but I like to look for these type of anomalies when things get weird.

Are you touching the targets the same with the playfield up and down, or are you playing games with the playfield down? I wonder if the targets are gapped a little close. So a light touch with the playfield up works, but a whack with the ball might shake things up enough to trigger multiple targets. If you touch the targets lightly with the playfield down do you still get multiple targets?

Could the roto target be a little loose so it shakes when it's hit by the ball?

Finally, if you can get it to work with the playfield up, try again and again as you slowly lower the playfield until it fails. See if it fails in the same place a few times. That might point to a short as @alexf suggests.