Mine did the same thing for a while. But easily fixed if you know where to look. Crawl under the drivers side dash under the steering wheel up towards where you radio unit is. you will see a flapper with a cable attatched to it. Or i should say , should be attatched to it. Mine came loose right there and while the vacuum was working fine, it wasnt moving the flapper. Seems to be a crappy way for it to connect, so i zip tied it so it wont ever come off again.
01 TJ. Dana 30/44 4:88's, 4.0 5 speed, 38.5x15 Boggers on 15x10 Streetlocks, CAI, B&M short throw, Neoprene Covers, 4" RC, 3" BL, too much to list and building. >..<