I have a 98 GS300 with 117,000 mi. Just noticed today I have the exact same problem? My AC is draining fine, but
when I lifted my floormat on the drivers side, I found it was soaking wet.
Used a wet vac, then pulled up the carpet and found standing water and the 2" padding was soaked. Dryed the floorboard
with a towel and ran a box fan for about an hour.
Next, ran the car in the garage with the AC on. After about 15 min, noticed water coming from behind/under the black rubber mat in the corner by the gas pedal.
That was great, considering I just got in back today from having the ball joints replaced.
I've loved my Lexus, but not impressed by these two failures.
I had the same problem on my 2000 GS300. Took it several times to the Lexus dealership and at first they could not find the problem as the car would not leak while in their garage. once they finally found the problem they wanted over 2K for the repair. Apparently the seal will wear out and the only thing they can do is replace the entire unit.
I finally took it to another mechanic (who only works on Lexus and other imports) and had them pull it out and re-seal it. It cost me $600 for the entire job. It's now been 3 years since they fixed it and it is still working perfectly.
Good luck!