Well,

As you said, the alarm is not disabled when you unlock the trunk.. so alarm goes off not at unlock time, but when you actually open the trunk or any door, right? And I assume that the trunk still unlocks all doors, right?

Regardless, sounds like a problem with your trunk lid lock switch or the wiring connected to it. Check the wiring to see if it looks ok.

Investing in the CDs or Alldata DIY (www.alldata.com) is a good investment for wiring problems.