You could have been poisoned of some type, that also causes fast travel to fail. !!!
or
Go and speak to one of the guards, you can still have a bounty without them pursuing you, and if nothing happens...
go back to the docks, talk to the captain and see if that works to go back to Windhelm.
and if that works, go and earn yourself a fair bounty.
Nothing too much, just something that hets the guards chasing you, give yourself up and pay it off
which resets the counter back to zero and allows you to rest/fast travel/sleep...
(Apparently it's something to do with a counting glitch in the coding that actually gives you a negative bounty (though it shows up as zero))