I was noticing this problem as well. I have noticed this with my phone sometimes, too. It always seems to work better while I'm holding it--with or without a case.
I have noticed a few other things: I sometimes like to use a rubber-tip stylus. Under similar conditions, the stylus seems to perform about as good (or poorly) as my fingers. For example, if I'm holding the Nexus with one hand, the stylus works alright. Holding it with both hands--works very well! When the Nexus is flat on my table (with the flap for my case behind it), it seems to work a little less, but overall works.
Also, I've noticed that it's almost strictly one side of the Nexus that ever seems to have a problem at one time. For me, it's the top half when I have it in landscape mode.
If I try to keep it suspended using the case flap, it doesn't work as well in either case.
So I feel like a summary of this entire forum might be:
Works best if you're holding it with both hands.
Works better if it is on hard flat surfaces--lots of connection to other conductors? Maybe pressure sensitivity?
Probably a manufacture defect.