Yep, there is something deeper here. Perhaps a fundamental flaw with pathing that has never been found. Or, if it is known, it's never been handled. Maybe this is really the true reason that Cryptic's corridors are the size of cargo bays? Just speculation.

I've been pondering this, perhaps more than I should but, I might have finally found an explanation. One thing I noticed when doing tests with Barrels was that it did flaky stuff more often if the game lagged while loading the map. Why? Another thing I sometimes saw was that the game apaprently sets items to hidden while setting up the map. Lag might cause the player to spawn before the items are hidden properly. Thus resulting in the player or Boffs spawning in the wrong place.

You can certainly see the invisible set load before it goes invisible, to be turned visible later. But, it's weird that it would move my boffs but not me at the same time.

I don't think that it spawns the player and boffs simultaneously. I've seen weird results on maps where a spawn point has enemies camping it. Sometimes you'll spawn alive and see that your boffs are already dead. I suspect that the game code treats boffs like regular AIs in some ways. Either way players and AIs use different rules in cases like this.