I have never had this problem in the closing mode (knock on wood) but I have intermittently had it in the opening mode and all I did was cycle the lever in the trunk and that fixed it.
I wonder if it is possible that the trunk lever mechanism or/slash switch/module is malfunctioning while in the closing mode causing all or some of these problems?
If you are able to open the trunk via the key during the malfunction give that a try, Id be curious...
2006 BMW 650i Sport/Premium Package
+ Various Mods & Upgrades