the seals are the first thing to check on older hybrids.
i have an '07 23SS and i check the seals constantly.
yours could be permanently compressed or cracked or torn.
second, is the door bowed in the middle?
third, check the marker lights above the bunk door. sometimes they will allow rain to get through the caulking.
fourth, are you sure no canvas got caught between the seals?
and Zoe the Wonder Dog(R.I.P.)
'07 Roo 23SS pushing an '07 Chevy Avalanche
Equalizer WDH and Prodigy BC