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I have a 2004 F-150 Lariat supercrew with the power sliding rear window and thought I had a window leak too. It turned out it wasn't the window leaking but was the third brakelight-bedlight located above the rear window that was actually leaking. Water would come in there and run down across the inside of the rear window. Took it back to the dealer for replacement of the seal under the light housing and that seems to have taken care of the problem. If you do a search here on this forum you will find several posts from others who have had a similar leak. When I took my truck in for repair the service manager said he just received a TSB on this problem so I guess its fairly common.
My brother does the warranty body work for the local Ford dealer and he has not had any 04 or 05s in for a leak around the rear glass. He had a lot of the older 150s though.
I too thought that my back window was leaking at first but turned out to be the brake light on the top of the cab. I took it in and they replaced the whole assembly and so far no more leaks.
My friends 04 fx4 did the same thing. He told it to the dealer and they replaced the rubber sealer and replaced his back seat because it had water stains on it.
I had the same problem...I removed the third brake light (two mounting screws hold it in place) and found the sealing gasket had been pushed out of place during assembly. If you are careful, you can peel the adhesive backed foam seal away and stick it back in the right place to form an effective weather seal as it was designed to do. There is also a small amount of sealant around the two mounting screws. It was just easier (and quicker) to fix it myself than to take it back to the dealer over in the next county where I bought it. I've had no problems since the repair. Interestingly enough the problem never showed up when I washed my truck...only when we had some really hard rain during the summer storm season.
I noticed my rear window leaking today while washing the truck. I believe it is from the light assy also. I called the dealer for an appt and he said he's seen several come in for the same problem.
my dad had the same issue on his...the dealer actually put a thicker gasket on the light....maybe ford has a replacement part but does not want to do a recall. you should ask the dealer....my dad went back 4 times before they got it fixed...finally the bigger gasket did it.