settimeout - how long is too long?

There shouldn't be... You can check by looking at Espruino's internals:

>setTimeout(function() {
:}, 1000*3600*15 /* 15 hours */);
=1
=[ undefined,
  { "time": 56599003766,
    "callback": function () {}
   }
 ]

time is the timeout in internal time units (1024*1024=1048576 on the STM32 Espruino boards), and you should be able to see if it's set to what you expect. It appears to work fine on mine.

Which board are you using? And are you using setDeepSleep?

An unlikely problem might be that there is some issue with the lower levels, which don't manage to wake it up at the correct time for long time periods.

To get around that, just try adding a setInterval(function(){}, 1000*3600) - it'll make sure the board wakes up every hour regardless of whatever else it's doing. If that fixes the problem we'll know that it is something to do with the lower levels - but it seems unlikely.