Check the simple things first. I had this problem once, and it turned out that the only problem was that a vacuum line had pulled off of the connector on the engine side of the firewall. 5 second fix.
Open the hood, and trace the vacuum line from the top of the engine back to the firewall. All of the other lines should also be hooked up (power brake, etc.) as theoretically one of them being open would let in enough air to keep your baffles from moving in the heater section.
Just one possibility.
1994 stock 260k mi