Do you have a mk2 or mk2a? How many tunes you have? More tunes = less memory for emphatic. If memory is low, stuff like this can happen. See if you see messages on your serial port when this happens...

Best thing I can recommend is adding ReserveCache=XX to your [Startup] section of config.ini, where XX is some number... Start with 8 or 16 and increase it if things don't get better. That will steal some memory from the player's cache and give it to emphatic.

The new version should be much better about a lot of this stuff, but, quite simply, the player doesn't leave much memory for apps, so we need to steal some back sometimes.