From what I read there is a possibility you blew the IBS on the negative terminal if you jumped the battery using a jump box. It does not take kindly to that kind of use.
I would not be telling the dealer about your non BMW HIDs because they can deny you CPO.
The charging system in this car is not your typical old style alternator-voltage regulator and battery. This is a sophisticated over designed system that uses an alternator- voltage regulator- IBS-DME controller. If you blow the IBS the DME typically drives the engine idle to a high state and you should receive a code.
You never mentioned if you are throwing a code or not.
Try charging the battery until it reads 12.6VDC and hope for the best...
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