The problem resolved itself for some reason.
Charged my remote for a number of hours today and it only charged up to 99%. Rebooted the ATV and still only at 99%. Is this some bug?
I wouldn't worry about that 1%
when any Apple battery starts to be in-sufficient like "only charges to 85%" i would start to worry. Battery don't maintain 100% ever.. They do loose charge at some stage in a lifetime as well battery icons can never be approximate due to software variances/checks... (I think) etc..
You'd find this happening more with battery that's been in use longer than a brand new one.