Yes, they made a change with MoP that kind of "layers" groups. Bear with me on the terminology, I don't really know what I'm talking about, lol.
There's the party, which you get as soon as you invite people. The second you enter a "combat group" {LFR, LFD, BGs(?) etc} you get converted to a raid, which layers over the actual party.
So now when you leave the dungeon or whatever, you're still in the "raid" layer. If you "leave" once, you can end up only leaving the "raid" layer, and you're still in the party, but can't see it because the rest of your "party" is still in the "raid".
Sometimes you could get everyone to leave once after the master leaves and suddenly the party frame would reappear showing everyone in a normal party. Or you can get errors while trying to reinvite saying all your slaves are still in group, even though they all look like they're out of group. That's them still in the second "layer." It was always especially visible if you logged out or crashed one one toon
Just have everyone leave group twice. I have a macro for /script LeaveParty() that I just spam a few times if I've done something that might mess up the group structure.
Here's a recent post talking about this weirdness with Flex raids -
http://us.battle.net/wow/en/forum/topic/10261776810
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