I dont have an answer, but I similar issue with my driver's side back door. In its case, it does not always lock. I have to open it up and shut it hard.

Per the manual, this is a sign that the door was not closed or fully closed. It is however. I can only assume something similar with the trunk. There must be a sensor/switch that allows action of the vacuum system to lock/unlock the door/trunk. And when that thing is out of line, there is a problem. At least thats my guess. I have not had time to look into it.

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1991 560 SEL / 185k miles
1992 750il / 17k miles - project car