I had almost the same issue. I purchased the car and found my trunk flooded after the first rain. The previous owner said he had recently had it repaired at a local upholstery shop. I called the upholstery shop and they said they would honor their work. I dropped it off the next morning. When I returned to pick it up that evening, the techs were checking it for leaks. To my dismay, it still leaked. They said I would have to drop it back off so they could try to figure out the problem. I took it home, disassembled the top myself and couldn't believe what I found. They had not used any butyl tape at all. They simply filled the gaps with at least three different compounds ranging from clear silicone bathroom caulk to black RTV. Needless to say, I didn't take it back. The sealing frame was broken in two but repairable. I cleaned out the mess and used some high density weather stripping ($3) in place of the butyl tape. After putting all back together, it hasn't leaked since and that was over a year ago. Here are some before and after pictures of their handy work…. Make sure you ask questions and if you can, try to be there when they are doing the work.
Last edited by Hornedfrog1969; 10-11-2012 at 08:50 AM.