This is a problem that started for me after using build 10130 for a couple of weeks and it's still present after upgrading to 10158. Long story short, while most programs don't have a problem being pinned to my taskbar, Skype and iTunes get duplicated if I have them pinned and running. By duplicated, I mean there's 2 icons, one for the pinned program and second for the actual, running program.
The current solution to this problem is, obviously, to keep both programs unpinned and just keep them running until the PC is restarted, at which point they need to be started again and put back in its place I'm used to having them on my taskbar. But I'd like to know if there's a way to fix this in a way that actually lets me keep these programs pinned.