Something strange just started to happen.. Whenever I try to enter an interior (ANY interior), the game just shuts down immediately. The problem disappears when I disable my mod.
I have no idea what is causing this.. I just noticed it today. The only things I have done lately is to add a few new creatures to a cell (a modified version of the red-eyed lich (I think it's related to a daedric quest) and a few Corruped Shades.

I might have done somehing else that I cannot think of at the moment.

Has this issue been encountered before? If so, what causes it?

"Deleted" NavMeshes? You can easily see by ordering the "Details" window by either Type or Deleted status.

did you accidentally do something to the base load door objects perhaps?

Ah, I do recall me deleting some NavMeshes last night (manually), or the night before. Don't remember really.

Could that be the cause?

Could very well be the culprit as they're directly tied to teleporting through doors. If you need to remove deletions, you can (in the details window) use the delete key to "Ignore" the "Deleted" forms. Upon saving/closing, those overrides will be removed from your plugin by CK. Might want to back up first before operating just in case that's not the problem, but you probably shouldn't delete any [00] stuff but edit it instead. For [00] NavMeshes, give them their FormIDs as EditorIDs though or the CK will (upon finalizing) replace them with isolated versions native to your plugin rather than merely editing the pre-existing ones.

but if it was navmeshes, wouldn't it only affect the areas where the navmeshes were deleted? he said it affected ALL interiors...

Not sure, but to have a NAVM in a plugin is to also have a NAVI which encompasses ALL NAVMs. If NAVI goes awry, crazy carp can happen including crashes.

That's what I did first, (pressing delete on the NavMeshes in the Detail Window) but upon saving/closing, nothing happened. They were still there. I reopened the CS, and they were still there. Redid it, nothing happened. And that was when I tried deleting them manually.

But I will try and poke around with this and see if I can solve, or else I'll loose a few hours work by reverting to an older backup.

EDIT: I deleted all traces of the NavMeshes from my plugin, and the issue still persists. Wouldn't the complete absence of NavMesh Data in my .esp file essentially mean that only the vanilla stuff remains? And that any NavMesh issues should be gone? Well, perhaps I am wrong!

Anyone?

Try saving out your interiors to another mod temporarily (Make a new mod, duplicate your cells with new names, then save out...then delete them from the Info area in the loading dialog, using the standard "Clean up" type procedure, then save out. If you still get this problem with your interiors all removed from your mod, then the problem lies somewhere else.