A liberal appllication of silicon should do the trick. I was having problems sealing pin holes in epoxy too, where the same problem pinholes wouldn't patch no matter how many times I went over it or what lengths I went to to prepare the surface. It was like these holes had positive air pressure pushing in or something. (was on concrete foundation) Once I went over those holes with silicon I was good to go.
While I was at it, I put a nice fat bead of it in all the corner seams, just to protect against any future cracking of the epoxy that might happen.