We have had the "funk" smell from time to time over the past year with no clue what was causing it in our 2008 Equinox. Finally opened up the back one day and found 3" of water in the spare tire well. For the most part, water only gets in when it is being driven. None of the carpets appear to be wet, only the spare tire well. Found the bulletin tonight and will be going through the various seals on the tailgate this week.
Really not sure what triggered it to be so bad the past few weeks. The "funky" smell has come and gone since we bought it 2.5 years ago and we could never figure out what it was since the smell was never consistent. What really surprises me now is it looks like we have some mold/mildew growing in the spare tire well now.

Once I "fix" the seals, going to have to bleach the well as best as I can. Not sure how difficult it is to pull the trim panels off, but that may be on the todo list as well.