You're not the only one folks. Same issue here, funny how when you get used to something...then it's different, it'll drive you mad.
I jumped back to 8.1 yesterday...simply too many things not polished enough for me.
Regarding this specific issue, I did chat with support online, they went through the steps, remove, reinstall, driver, etc.,
Asked if I changed the "Watch" battery, I told him less then 24 hours prior, everything worked perfect.
He said he could send me a new pen, which...I was ok with, but this was a W10 issue, not a pen or battery issue.
I got the top button to open the Metro OneNote. Double click screen shot to MON. The bottom button worked for eraser in MON.
The only button that worked for me in OneNote 2013 was the right click (middle button).
If ON was the only issues I experienced, I could easy stay with W10. But that was just the tip of the iceberg for me...
I'd bet in the next 2 weeks many of these issues get resolved. It is my opinion MS is working on polishing/refining W10 on the SP3 for a SP4 release.
I'm a little disappointed it's not more refined for their flagship device.