For anyone reading and wondering what happened with this, some pens, some batteries, a very reproducible problem and two SP4s later an online chat with Microsoft confirms this is a known issue to them that occurs with the i5 8 gig 256 model. A firmware fix is in the works potentially this month (February); I had the CS person repeat it to me twice.
Kind of reminds me of I think it was the first iPod touch where there was this wifi problem (but in that case Apple never did acknowledge it) that caused me to send two back then a firmware fix miraculously fixed the issue on my third one for me and a few hundred other people discussing it on an Apple forum thread at the time.
There's not much you can do about the SP pen problem in my experience but you can try the volume button restart thing or deleting the pen driver then restart your device and it will reinstall. What I mainly do is when the pen quits, reverse it immediately so the eraser re-engages it. Works a lot of the time. When that fails, I revert to a finger and just wait. Pen resumption pen time after that varies.
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