You probably had some chemical interaction between the paint and the resin. Wax, no matter how many coats you apply, is unable to block reactivity between the plug/mold surface and the fresh resin used to make the mold/part. PVA (polyvinyl alcohol) could have been used to block this reactivity. The purpose of using PVA is to create a barrier between the plug/mold surface and the fresh resin. Wax provides slip. PVA blocks reactivity. If you don't want to use PVA you need to do lots of testing with plug surfacing agents and your resins to make sure that no reactivity will occur.

BTW, the first coat of wax provides the most build up. Subsequent layers of wax are about 1/20 of the thickness of the first coat. I usually only use 4 coats of wax + PVA. In theory you only need 1 coat of wax. The reason most manufacturers recommend 3 to 5 applications is to insure complete coverage.