I've had this issue as far back as my SW class a couple years ago, but I would really like to figure out what's happening now. I'm trying to populate a lot of LEDs using copy with mates, but many parts are flipped. I can't see any possible reason why they should flip.

Also, when I try to manually flip them, it seems one part is mated to another part in a daisy chain, and that's definately something I don't want. They should all be mating to the underside of the panel just like the first one. Why are they mating to each other?

These all move together as one (below)