Several sites have reported some issues with inputs from the JoyCons intermittently lagging when using them not attached to the system (ie. when the Switch is docked) in some situations. Andre at GameXplain did some testing (video below) and it appears to be a matter of the signal strength just being weak.
From personal experience playing the Switch at PAX South, I didn't run into any problems, but I was standing/sitting only a couple feet away from the system at the most. These problems seem to be from people now using it in a more traditional gaming setup with the system sitting near the TV several feet away.
Disappointing, but hopefully this is something they can fix with a firmware update maybe to boost the JoyCon signal strength. Dunno how feasible that is though.