I can't find mention of this in the What's New, but I'm sure something odd has changed in unshelving in 2016.1.
When I go to unshelve changes, sometimes only one copy of my change (in my project's /src dir) is unshelved. The one in /public doesn't get unshelved. Is the part of the dialog where you can select specific files to unshelve new? In any case, I make sure all files are ticked, but sometimes not all are unshelved.
Also, I'm sure the checkbox to 'remove successfully applied files from shelf' is new. Again, there seems to be inconsistent behaviour with this. But one thing is that if I check it, sometimes a copy of my shelf seems to appear with 0 files.
I can't work out the logic to all this. It used to be that unshelving 'just worked'. Now all sorts of confusing things seem to happen. Maybe I'm using the new features wrongly but I can't find accurate documentation explaining what's changed.