[-Ramirez-]

I think the "problem" is completely related to AP. I'm not even sure it is a problem.

When you get a "full heal" in a GC level or by some other means, it allows your HP to bet set higher than AP restrictions would normally allow. So if you have 0 AP, you'd normally be capped at 3 hearts, but a full heal would set it to however many hearts you've obtained via quests. When you exit a GC level and enter a normal level, it puts you under AP restrictions again, so in the case of 0 AP, you'd drop to 3 hearts. Are you sure this isn't the behavior you're experiencing? That doesn't really explain the pause thing, but since no details about the location or AP were given about that situation, I can't really know what could cause it.