This just happened to me. I opened the trunk with the remote and closed it immediately (if you do this quick enough, it will not lock the first time because the solenoid is still opening the trunk, that's what you want to do.) I did this a few times and the alarm now works fine.
Funny thing is, the light on the dash was not showing the trunk being open. It could be they are using two different switches for sensing if the trunk is open, and the alarm switch was dirty. Anyway, all fixed.