Had the same problem on mine after the dealer replace the wood trim around the shifter under warranty. They put a new boot piece on and it did would pop off every time I shifted too. Put a third one on and it's been fine. My guess is that the leather is stitched too tightly to save $.05 on an extra 1/16" of material.

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'04 E53, 4.4 Sport
'97 E39 528i
'86 911 Carrera, track car
'96 BMW R1100R