When using playMusic [name, start] to start in the middle of custom track defined in description.ext, ARMA loses track of how far into the music it is when the player alt-tabs. This only appears to occur for tracks above some length (a 3 minute track didn't have this issue, while 7, 12, 15, and 29 minute tracks did), but when it does occur, it happens 100% of the time. This reset only happens the first time the player alt-tabs, and it appears that it always resets to an earlier part of the song.
I haven't been able to reproduce this with the in-game tracks, but that may be because none of the tracks I tried were long enough.