I thought that I had seen a post where someone else had the same problem, the caulk between the glass and frame had opened up.
I remembered "small boy" and searched and found this:
Look at the one where there is a picture of the quarter window and words like spray water here.....
Permalink #73. He has another post on the next page and indicates what he did fixed his problem.
2001 Red CVT
19,351 miles lmpg 19.0 as of Oct 7, 2011
Best tank 78.9 MPG, 738.9 miles