I had mine plugged into the quick charger last night. Saw the charge icon, so I thought it was charging, but when I woke up this morning, the bar hadn't moved. I did a Power Off, and now I'm charging it that way to see if it makes any difference.
I also seem to be having issues with the rapid charging dock. It was the best with the Developer Version of 2.0, never had an issue with 1.0.7 but now I have to watch for 5 seconds or so until I know its actually changing.
If its not charging I wiggle it a little on the dock and it works fine.
It's not likely to be the software though... this sort of thing is almost certainly the charger, and those lousy little pins that don't line up. Have you checked yours to see if it's off?
As Peter noted, the spring-loaded pins are most likely not all extended to an equal height.
The non-dock Rapid charger is easier to adjust since there is no dock-framework restricting slight adjustments that allow the magnetic plug to fit better. Peter and I have both posted pictures in other threads showing the issues (mis-alignment) of the pins.