anyone else having a problem with these... I place one and then teleport to a gate and it automatically picks up the pyramid I placed and puts them back in my inventory...

This is a known issue. It only happens if you teleport to somewhere not on the current map.

I don't know if this is intended behavior though. I hope not.

It is intended. The pyramids specifically state that if you go too far they will automatically go back together.

It seems the main purpose of them outside of puzzles is for people playing co-op to quickly travel to each other.

Well - they are very handy if you are wandering about and want to pop back to town to visit a vendor, maybe pick up a skill book etc.