Bados, I have the same EXACT problem! Have you found the problem yet? I'd LOVE to know when you do!
I found this posting of others with the same problem... and possible solution! A/C condensation tube blocked or disconnected... doesn't sound too pricey to fix.
ptdoityourself.net PTDIY.net - PT Cruiser Technical Library Part Fifty Four Q&A 1326 - 1350
Here's the text from the above (which is located about 3/5th DOWN the url address above):
Q. "We have a 2001 LE PT with 50k miles. Water gets into the rear passenger side floorboard when it rains. How can I track down the source? Could it be the sunroof drain? If so where is that drain and where does it run?" – Clay, from Alabama.
A. If you discovered water on the front passenger side floorboard I would suggest checking the A/C condensation drain tube for stoppage. Make certain that the water you see in the rear passenger side area does not originate in the front passenger side area.
If it originates in the rear area it is not likely that the sunroof is causing the problem given the position of the drain hoses and condition of the headliner. Adequate drainage is provided by a drain trough in the sunroof housing which encircles the sliding glass panel and leads to drain hoses. If a wet headliner or other water leak complaints are encountered, ensure that the drainage system is not plugged or disconnected. The front drainage hose is routed through the A pillar and exits in the passenger side cowl area below the windshield. The rear drainage hose is routed through the back of the vehicle under the headliner and exits near the passenger side liftgate hinge.
Other than the A/C and sunroof drains the issue can be caused by a number of factors and can be time consuming to resolve."
PLEASE let me know if you find a solution.