I have just had this under Win 7.
$ git stash poperror: cannot stat 'parentFolder/subfolder': Permission deniederror: cannot stat 'parentFolder/subfolder': Permission denied
Diagnosis:
1>I went to the subfolder and it's there and I couldn't delete it !
2>Use "process explorer" -> Find -> Find handles and Dlls -> put the "subfolder" name there and search.
Result: It turns out it's XMLSpy has opened one of the xml there, close XML Spy and try stash pop again, it's working now.