I'm in the train station now (single player) and something new has started happening. Seems like an old Quake3 engine problem to me.

People (and dogs) have started partially appearing through doors (say just a hand or face). The problem is dogs can bite me if I try to open the door, and soldiers can shoot me from down a hall (from behind a door).

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that happened to me as well, only on one mission though. I updated while in that mission, and I think the update altered it and the mid level save could have had conflicts.

Interesting... I had just recently applied the patch.

So, it cleared up for you after the level you were on?

Yep. Just dealt with it for that level, and it went away afterward.