OKay... first, you can get rid of the problem of the cooldown bar wrapping around and overlapping the HOT/DOT bar using this command for your DK...
/nui hud cdmin 10
(that also works for hunters who get a wrap around when the drop a trap)
As for the issues with your cooldown counters and spell durations, have a look at this FAQ and see if it clears anything up before we go trying to run down a bug:
http://www.wowinterface.com/forums/s...ad.php?t=31929
I *somewhat* certain that cooldown timers and spell durations are working correctly in 5.07.04 (Development)