I have been having recurring issues with my 2000 E39 528i. Here is the sequence of events:
May- had the thermostat housing replaced to correct a coolant leak
Late June- Car went from operating fine to being undrivable while sitting at a redlight. Had to get towed to the shop. The error codes indicated that the throttle body needed to be replaced. Replaced Throttle body
Two weeks later - Service engine light comes on, car feels like it is missing when accelerating. Told the Cam sensors need to be replaced. Replace both Cam sensors
Two days later - Car has been driving fine. Start it in the morning and the service engine, ESC, Brake, and EML lights are all on. Car will not accelerate past 45mph and feels like it is missing. Take it to the shop. The mechanic shows me that the pedal sensors are giving two different readings 1.5 degrees apart. After two hours, the error code changes to say the Cam sensor are bad again. Without doing anything, the lights all go off and the car now runs fine.Mechanic thought it could be a pinched wire somewhere that was causing an intermittent short, but didn't really have any concrete information. Any ideas? Thanks

I hate electrical gremlins, this sounded like one

Check the battery for low voltage.

voltage is 12.4 when off, 13.6 when the car is on. Is that low?

You're definitely on the edge there. A healthy battery generally has a voltage of 12.5 or more with the engine off, and about 14.0 volts with the engine running. The correct range is 13.6 to 14.4 volts with the engine running.

Jim Levie or one of the other real gurus on here might be able to provide you with more guidance, but low battery voltage causes a host of bizarre problems on these cars. I don't think it accounts for all the problems you've had, but I'm going to venture that it might explain the latter. Have the battery thoroughly checked - you may have a cell that's shorting.

Other possibilities that are not unknown for these cars are a bad ignition switch (the electrical portion), though the symptoms are usually a bit different than what you're seeing - usually, you'll have problems with the radio, cruise control, dash lights and steering wheel height setting. A bad ground can cause headaches as well.

Here's an article on the Roadfly board that you might find helpful: http://bimmer.roadfly.com/bmw/forums/e39/7901708-1.html