I haven't checked the rubber stops yet, but think this might be related to the ubiquitous convertible glovebox issue.
When I bought the car, the glovebox was stuck closed. I was able to get it open with a small screwdriver, between the inner and outer latches, pushing the latch lever up, which released the glovebox.
I took the latch apart, soldered a loose wire to the micro switch which locks out the trunk, reset the worm gear drive, and reassembled everything. I can now open the glovebox only with the key, it opens on its own sometimes when I unlock the car, and I've got this problem with my trunk.
Long story short, when my trunk fails to latch, I've found that if I hit the trunk latch button on my key and then close the trunk, it latches.
I love my Bimmer. It's more challenging than my wife.