My last Wrangler had a lot of water inside both the front freedom panels right off the lot (used 2008, with only 15,000 kms, not even a scratch on it). There was a pin hole sized defect near the where the rubber seal meets the flange, on the back edge, on both panels.
I traded it in towards a new Jeep after 2000 km of dealing with the sloshing and the stink (the worst!!!) that came out of those panels. I don't know it it was ever fixed, or just sold with the soft top only (probably).