Maybe the trunk monkey is leaving it open too long when he gets out in the rain?

Any pics of the locations where it's getting wet? Someone else may have seen a similar thing.

 

Do you have a hatch or sedan?

On my '03, I noticed the left side trunk liner was slightly damp after a lot of rain. I swapped my trunk, so the trunk was very slightly misaligned (still able to close, though). I loosened the mounting bolts and adjusted it slightly, and that fixed the leak.

Check all seals, and check underneath the carpet for signs of rust, etc.

 

Sedan.
I'll look over it, more when I have some daylight.
I thought there might have been a common spot.
Thanks for the replies, I appreciate it.

 

The trunk seals are kind of crappy. I had issues in hard rain. Apparently water was getting under the seal. I pulled up the old seal,cleaned it and used some silicone sealer to attach it back on the trunk lip. I also shaved a tiny bit off the trunk bump stops and readjusted the latch so the trunk lid would compress the seal a little bit more.

 

I had a similar problem on my 05. Turned out the dealer I got it from didnt reseal the trunk very well when they replaced the third brake light in my wing. Like Donkey said I would check the seals