Trunk Leak Leads to Serious Funk

After noticing a bad smell in my car (a 2001 Mazda Protege) beginning Saturday morning, I finally located its source today: about three inches of liquid that were in the right quarter-panel well of the trunk (where the jack is stored) that appeared to be fermenting or something. Now, let me preface by saying I have NOT spilled anything in the trunk lately (just about 1/2 a cup of vinegar on the other side of the trunk more than 3 months ago). Here's the timeline:

Friday -- very, very heavy rains
Saturday morning -- noticed smell after car was parked overnight in garage(like funky cheese, very unpleasant, but not musty/moldy)
Sunday, Monday, -- smell worsening, couldn't locate anything in passenger compartment
Tuesday -- smell even worse, discovered liquid in trunk.

The liquid was actually yellowish-white and cloudy. Once I absorbed the standing liquid, there appears to be a cottage-cheese like sludge at the bottom of the well. I really can't figure out what the cause might be -- the only thing I can come up with is a seam leak (which seem to be common in that area) that has somehow caused the caulking to disintegrate and stink? It just seems odd, because it is a very organic smell, not a chemical smell. The trunk mat (and a piece of carpet remnant I had on top of that) were not wet, so I don't think it was a problem with the trunk weatherstripping.

I've got a call in to my insurance company b/c I was rear-ended several months ago and I think a poor repair job may have caused the leak, but that still doesn't explain the smell. I'm afraid they're not going to believe me when I tell them that I haven't spilled anything. Has anyone EVER encountered something like this?
 
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There's only 3 places that I know of where water can get in there...the trunk opening seal, the wiring conduit (if the Protege has one) leading from the lid to the trunk gutter, or the least likely...through the taillight. What I would do: Clean the weatherstripping and the underneath surface of the trunk lid where the seal meets it. Then, apply something to the entire seal that will leave a mark on the underside of the lid when you close it. (Vaseline, grease...whatever you want that will transfer from the seal to the trunk when they meet) and see if there are any spots where they don't meet when you close it. A repair in that area could have been done incorrectly, causing a gap between the seal and the trunklid.

If you can't find it yourself by any reasonable method, I'd take it back to the repair facility and let them track it down.
 
i found water in that area as well, and tracked it to a seem behind the tail light on that side.
my solution was to remove the tail light and just put some silicone caulking around all the seems i could find and reach. problem has been gone since then.
 
Thanks, I'll check the trunk seal. Any thoughts on the smell? I've never heard of caulk doing that, but don't know what else could be causing it.
 
My taillights leaked for a while depositing water into the hatch, until my rear seats got wet...Now my sunroof weather-stripping must be going, cause now my headliner is all wet....damn rain, and no garage=pissed off me...
 
any standing water = funk.
especially if there is lousy air flow and its doubtful that that part of your trunk is the cleanest thing ever. take care of the water and if theres still a funk, see if you can track it down.
 
Ditto on the water and the funk. After heavy rains one day. I noticed water standing in the spare tire well and in the jack area. Took a quick look and it seemed like it was coming from the tail light. I need to take a better look to see exactly where it's coming from.
 
I didn't experience any funk, but the first time I went to get my jack out of the trunk (I bought the car with 80k mi.) it was all rusted out. I knocked most of it loose, but it still was a pain to jack a car up with a rusted out jack.
 
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