May not be the same issue, but...
I would end up with more water than I thought should be in my boat by the end of a run so I checked for cracks, holes, loose screws, etc, but found nothing. I made a run where I didn't roll, on purpose or otherwise, and found the boat dry. Even though the tunnel of the skirt fit tight, there would be some water leak down between the fabric and my abdomen.
Again, it may not be the same issue, but maybe it helps.