Double check your battery's negative connection. It is possible that you have not made a good connection. When I take my negative cable off my trunk won't close either. I have to press the button on my remote to release it and then it closes properly. I don't have the other issues you mention though.

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[Sold] 2004 X5 4.4i - Sterling Gray - Truffle Brown, Sport, Preminum, Rear Climate, DSP, Sirius, PDC, 132's (19 inch wheel), Comfort Seats
Dynavin, JL Audio Stealthbox, Alpine PDX-5 Amp