I had a similar problem with the stitching and a couple of worn spots on my popup's slide out tent vinyl canvas.
I used a product called: http://www.sunnysports.com/Prod/MCNSG.html
It worked awesome. I then treated all the stitched seams and some other worn areas where it appeared thinner from looking at the tents from the inside.
It drys clear and you couldn't even see it. I had zero seepage or moisture on the stitching or otherwise after using it. Good luck