I'd love to be able to reproduce it, but it's never the same twice. Not to mention, my light shows aren't "simple." If, as previously explained, it's all dependent on what the CPU is doing at the time, then it's just a matter of luck as to when things do and do not line up accurately.
I have been using this software for years. I have used it on three different computers. One was a jacked up, powerful editing PC, one was an Apple MacBook, and the one I am currently using is a dedicated PC laptop that is used exclusively to run my light shows and does NOTHING else. No anti-virus, no updates, no internet, no other programs. Every one of these systems had the same syncing issues crop up.
The closest I have come to a "fix" for this is to make sure there is a second of silence at the beginning of my audio WAV files. In that brief silence I put a little "pause" block so the timeline stops while technically "playing" the WAV. For some reason, starting the file and then pausing and restarting it seems to (usually) minimize the occurrence of out-of-sync operation. I assume it's because the program and the CPU have a brief moment to kind of "catch up" to one another. Just a guess though.
It seems like a silly workaround for a program that's supposed to just work but, really, there aren't any other alternatives to it. Maybe that's why it's a bit rough around the edges.