The micro skips happen for me using BubbleUPnP and my Primare NP5 streamer as well.
I mostly listen to playlists made up of mixed tracks. I'm not exactly sure how the buffers work in the DAC but I'm thinking that each time a track changes the buffer clears information from the previous track and then loads information for the current track. Watching the seek bar counter, the skip happens consistently at the 10 to 12 second mark. Is this where the buffer clears?
@igotdibs are you an album start to finish listener or a playlist of mixed tracks type listener?
I would think that due to the gapless playback of an entire album, there would be only one buffer clear/load cycle at the bigging of an album and may explain why this problem isn't more widely reported? Most listeners are likely ones that play an entire album from start to finish.
The only variable that has changed in the new firmware that could cause this is the changes to the buffers (except for changes done to improve latency) so it seems obvious to me that this is the issue. Then again, I could also be completely out to lunch.
I've passed my theory on to Vinshine and also requested the files to roll back the firmware. Vinshine/Denafrips isn't convinced yet that it's a firmware issue.