Bumping this as I've had the same issue with my Nexus 5 for ages. Every time I click a number to dial through gmail or chrome, it asks me whether to complete action using Phone or Skype, even though every time I choose Phone and "Always". Same thing for opening web pages (Chrome and Dolphin), opening Instagram links (Instagram or Chrome), and anything else I have more than 1 app for.
Running stock 4.4.3 rooted with CF-Auto-Root. I've recently completely reset my Nexus 5 and reinstalled everything from scratch, and the phone is still not remembering default app settings.
Is this an issue with rooted phones only? Or is it a sign of a hardware defect that I should be requesting warranty service for? Anyone gotten to the bottom of this?