Well, I'm no expert on this but this does not sound like transponder or imob issue. If the starter is turning over but the engine does not fire up then there is some other fault. There could be a whole host of things from fuel pump (think there is a cut out switch somewhere) all the way to one of the sensors has been unplugged or damaged.
In the UK BMW charge around £30 to perform a diagnostic on the car, so if the conversion is anything like our gas prices means it will cost about $5 for you (! sorry, hard to keep the bitterness under control - 70% tax is reasonable I'm sure). Coming back on to the point, I would say that the garage that did this to your car needs to get your car recovered to a main dealer and pay for the diagnostic (not to mention the repair). Presumably they are providing you with a replacement hire car.
It is possible to purchase a serial cable for a laptop that plugs into the diagnostic point in the drivers footwell and use sw to read and even reset the fault codes - but this should not be your problem. If the engine attempts to start and fails, a fault code and reason will be logged in the car.
Good luck, if you can let us know what the problem is it would be great.
