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The first thing coming to my mind is a bad thermostat. They are supposed to fail-open, but I've seen the opposite. If that happens, the cooling system basically ignores the radiator and operates in a closed loop. Radiator may be warm-cold (at least at top), while engine is cooking. Turning on the heat usually blows very hot air and may cool the engine down a bit since that circuit is usually on the engine side. If the sensors for the fans are in the radiator, fan may not come on (unless AC is turned on).
I think your t-stat is both electronic and mechanical. If you have a code reader, it might give you some hints.
That said, are you absolutely sure you bled the system properly? I don't know the specifics of the M54 but the N52 has a very specific bleeding method that has to be followed - I'd imagine its predecessor would be similar. Sometimes air can get stuck in different places and give you all kinds of hell.
I don't think I have to tell you that it's not smart to drive the car anywhere (even limping) until this is fixed, especially since your engine is made of aluminium.
good luck,
-gc
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