Yeh, that could be it. I know a little hint to make that part easier, too. When you first get in there (the first part, not the secret part), you get all the muds attention and tell them to follow you. After you have done this (Im not sure if its just for PC, but) Quicksave. Pull the lever, and run into the next screen being careful not to hit the wall, as it wastes time, so stop running just before you go off the ledge. Then when youre in the next screen, run into the next screen after that. If this was done correctly, the Muds should not be hyped up on laughing gas, which makes it easier to get past the bit with all the doors and stuff. If it wasnt done correctly, reload it from the Quicksave you did and try again.
If that doesnt make sense to anybody, tell me, and Ill attempt to rewrite it.