Broken clutch disk can cause this. I just fixed a Honda element with the same problem, I could put it in gear not running then start it in gear. No shifting while running though. Clutch pedal felt fine too.
1989 Jeep Comanche 4.0L 5 Speed 4x4 Long Bed 4.10s LSD
1991 Jeep Comanche 2.5L 5 speed Red Short Bed