I'm also using with a shield, and have an almost identical setup to the way you are using it.
I noticed that it was freezing up regularly using the back button, but that just popped up over the last few days. I barely use my Skip, sadly, because it's just not that good (I have another remote I use with my FLIRC USB and it works flawlessly, without needing complete line of site.... the Skip needs to be pointed "just right" in order to work. So I thought it might be batteries, replaced those, still having the issue. Finally, I synced today and upgraded the firmware to the latest, and that does seem to have fixed it, but it still doesn't make sense how the freezing was not an issue until recently.
I also noticed that the select button (using the Shield profile for it) doesn't work on the on screen keyboards in native Android TV applications. Not a huge issue, because I always have my phone I can use to send text, but it is a little annoying. I suspect that is an android issue, not a Skip/Flirc issue.