I also have problem since Oct 13,2016. No data upload from Garmin to Nike app.
After multiple dis- and reconnects it finally stabilized for my accounts too. I appears that Runkeep did indeed change something on their side because they did send me a few emails pointing out the deeper Garmin integration and even requesting feedback.
If I had to guess this might be because Garmin people moving over to Strava (like I did myself) due to the better integration of segments, beacons etc.