When using appfinder or thunar(/usr/share/applciations/) to Drag and Drop launchers to the panel, the whole command is suffixed with ''. So thunar would be 'Thunar %F' instead of just Thunar %F. Editing the launcher and removing them of course solves the problem.
Wasn't sure what to file under, sorry.
Wow, this one is still there. Confirmed on rc1 and proposed blocking-4.6
Fixed in revision 29534.
Note that names with a space are still broken... that's why the escaping was here, didn't really work tho.