I used to get this all the time, the solution is simple, though not preferred, it works perfect. Write down each timecode that is giving you this problem. Go into the .ssa manually and edit each of these lines to give the endtime a little more duration after the start time (you'll notice they're really close when you look at the lines). Save the .ssa and retry it in MaestroSBT. You should have no more issues and your subs will be in perfect sync (except for the timecodes you modified, they will now stay on the screen a little bit longer than usual)