Your 99 "should" have the same switch setup as my 98 and my FSM shows the liftgate ajar switch is a "push-in" type, just like the doors, located right above the latch mechanism. Also, as tomk pointed out, the wiring diagrams show the wiring to the switch also feeds a "liftgate ajar sense input" on the CTM (which controls the dash indicators.) From your symptoms, I'd say this switch is "barely" making contact when the hatch is closed and vibration from the new speakers is rattling the liftgate enough to causing the contacts to open up.
So, unless we're talking "earthquake level" bass from the speakers, I'd say Steve's right and the latch (or possibly the switch) needs to be adjusted a bit so it makes a more secure connection when the hatch is closed. It's also possible the screws/nuts holding the switch in place may have simply loosened up and just need to be tightened back down??
Note, as you can see from the attached image out of my FSM, you'll need to remove the lower liftgate molding to get at the switch.
Good luck!