So last night I was killing withers, I was getting a decent amount of them (1 every minute or so - Quite low on average TBH) now today, When I log on - I run around for 25 minutes, not a single wither, I know the fortress is a 1.4.2 fortress as I was killing them there yesterday - Are they broken?
Yep that is the problem causing them to not spawn. Essentially, every reboot breaks wither spawning fortresses. I suggest you hold off on looking for them until Bukkit fixes it.