MechJeb doesn't calculate fuel flow properly when you have a powered external tank, that refuels an adjected internal tank, that is not drained directly by engines but has an inactive engine adjected.
My spacecraft is a Space-Shuttle like spaceplane with one middle atmospheric engine, that's not used during ascent. The external tank is connected to my middle fuel tank on the spaceplane. This middle tank has circular fuel flow with the both adjected side tanks, that store an aerospike each.

This prevents the ET to be jettisoned automatically when empty

Can you upload your .craft (pastebin is good) to save us the trouble of building something similar? =)

Ok, I allready figured out the problem, it was my fault.
Sorry for that, a fuelline didn't connect properly
Therefore my last stage isn't jettisoned as it contains disabled engines, is this intended?

Stages are kept as long as there is fuel or useful engines in them. Not sure which one applies in your case, but reopen this if you see anything else wrong.