Problem with setTimeout() and deep sleep mode

Actually setDeepSleep doesn't sleep immediately, it just sets a flag. You only actually need to call it once in the whole program, so any subsequent calls don't do anything.

I'm not really sure what the issue could be - my only guess so far would be that it's using the external real-time clock, and that it's unstable - either stopping, or oscillating wildly causing time to run too quickly. It's just a guess though - it's very hard to know anything without a bit more info.