I've got the same problem...
I found a small pin hole in the silicone that is directly under were the jack is kept. I had to remove the carpet and do quite a bit of searching to find it. The problem I have is when its been raining the water comes up from under the wheel well, and finds it way into were the spare tire is kept. I've just cleaned it up and added some silicone back to it for now, until winter is over and I can properly repair it.
If that's not your problem, maybe the weather stripping has come loose somewhere around the trunk.
I found a small pin hole in the silicone that is directly under were the jack is kept. I had to remove the carpet and do quite a bit of searching to find it. The problem I have is when its been raining the water comes up from under the wheel well, and finds it way into were the spare tire is kept. I've just cleaned it up and added some silicone back to it for now, until winter is over and I can properly repair it.
If that's not your problem, maybe the weather stripping has come loose somewhere around the trunk.