Ah've found, that if the counter finishes between 00:00:01 & 00:00:59 (ie between 1 and 59 seconds on the SWClock) it will restart the timer at 59 seconds, so best bet would be to wait for the next whole minute before checking
Maybe ah didn't explain properly: what ah meant was, if the full countdown has finished but the game clock hasn't completed a full minute (ie the seconds are not 00), at least that is what ah've found recently when ah started paying attention
I don't think that matters in this case, as so many timers are looping for so many things (sublight travel, crafting, force training, etc, etc) that it's just a timer bug.