I've noticed the same thing and came here to see if it's an known issue...
In my case, I re-armed to 4x ext aux tanks, I jettisoned two of the tanks, noticed I still couldn't generate enough lift before over-torque, then jettisoned the last two tanks, still can't generate enough lift for vertical or rolling takeoff.
I was sitting idle on the ground when I jett'd both sets of tanks and didn't notice any kind of physics response (suspension rebound, etc.) or anything like you do when they load them during a rearm.
EDIT:
Tested with possible workarounds.
- spawned Cold and Hot with full internal fuel and 4x ext tanks, pulled pitch to about 97-102% torque to start picking up, get to about 12 ft and unable to maintain vertical climb.
Land, jettison all four tanks, and try to pick up again--same performance noted
Land, open rearm dialogue, "remove payload" from all four stations,and try to pick up again--same performance noted
Land, rearm with all HE Rocket pods (trying to replace ghost payload?), try to pick up again--same performance noted
exited mission, re-launched hot with all HE Rocket pods--no issues picking up, pitching a bit ETL, climbing at about 90% tq
ApacheFuelTanksHot.trk