How odd...
Have you attached any scripts directly to them? Perhaps a script is resetting their positions?
I've never had this happen to me, my NPCs always point the way I tell them to...
Do they always face a certain direction? Have you tried placing them near different walls to see if they face them?
If they always face a certain way, you could try placing them on the opposite side of the room. Maybe that could help.
I've heard of modders having trouble with NPC positions when they aren't placed carefully.
As a tip, make sure that anytime you place an NPC, you place them slightly above the floor, rather than directly on it.
Morrowind has some minor issues with collision, which can cause problems for "live actors". (Creatures and NPCs)
For example, the infamous "floating glitch" which can cause some NPCs in interiors to literally "float away".
(Like Sharn gra-Muzgob, which can break the early parts of the main quest, when/if that happens.)
(Note: Accoring to the UESPWiki, the "Morrowind Patch Project" fixes her glitch.)
I don't know if that is the cause of your problems, but it's still a good idea to place NPCs slightly above the ground.
Morrowind's engine will put them down on the floor properly for you.
(Don't place them higher off the ground than about half a foot, though.)
I hope this will help you. ^_^
Edit: It looks like Pluto ninja'd me.
I figured you would have already done that.
But yeah, you should be sure to properly path-grid your cells, especially if you have complex cell layouts.
A proper path-grid should help you with the NPC positioning as well.