Very strange, I tested it both for backward compatability and fresh install. Something is different on my PC then.
Can you try deleting AffDots.lua and AffDots.lua.bak files in "WoW/WTF/Account/%YourName%/SavedVariables" folder?
One thing I noticed on training dummy - when Windsong haste procs, UA damage is not updated. That is because while haste increases dot dps (by ticking faster), it does not increase it's overall damage unless it gets to a breakpoint. So optimally addon should display dps instead of total damage.
Also I have full intention to add timer for procs/buffs, otherwise they can be wasted if you refresh 0.01 second after it has expired. Some kind of timer with "window of opportunity" I guess. Plus more customizable layout, not fixed sizes/positions as it is now.
Agony not refreshing bug is tricky, there are occasions when dot application/refresh does not appear in combalog. It is possible that it cannot be fixed.
Unrelated: In case someone wonders just how bad it is to allow Agony to drop, it is the same as losing 3,6 ticks of 10 stack Agony.