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Crazydaisy's son here...
I had this problem in Marine Episode 6 Hangar somewhat but fixed it mostly by just restarting the mission, and I should note I had to restart it a couple of times to get it to work. However I hadn't found ANY way to fix this problem in Predator Episode 6 Battle and was going to ask for help but I found a potential solution, at least it worked for me.

What happens is that the Queen simply runs into the walls and won't do anything else. She doesn't attack or anything...just runs into the walls like she is drunk, lol. This is ALL she does in the Predator Episode, but in the Marine Episode she randomly does it.

I got the queen to work properly in Predator Episode 6 Battle and more efficiently in Marine Episode 6 Hangar by setting the AvP_Classic.exe, located where the game is installed, to run in Window 98/Windows ME compatibility mode and by checking the box at the bottom to Run this program as an administrator. You should probably start it with the .exe and not a start menu shortcut or otherwise.

Hopefully this solution will help anyone else with a similar problem.