I'm having some issues with my weakaura during kromog encounter. When i'm in hands, combo point dissapear :x
I'm using this WA : http://pastebin.com/bWmvBkSz
I don't have the WA, or anything, but things like hands can have strange implementations -- it might be using the vehicle code, which sometimes causes things to "behave" and not show, eg, combo points that you can't use while in a vehicle. Except in this case, randomly, your stable daily quest mount, or maybe the hands on Kromog, are not stopping your normal rotation stuff.
I don't have a fix, but until you find one, you may consider using compo points redux or shadow unit frame or something like that to display your combo points.
I've got the same issue where I'll be able to see my Anticipation stacks on the WA, but I'm unable to see the normal combo points. I just enabled the Combo points in SUF for my player frame and simply just look there during the hands.