I installed the plugin manually, and tested it. No GUI problems anymore, and I could select all 5 radio-buttons for the given selection options.
One remark though:
when the last annotation file is removed of a sub-folder, that sub-folder still remains and hence, could be removed as well. The same applies when all sub-folders are removed within the main folder ANNOTATIONS, that latter folder could be removed also (as is done when selecting the "All" option)
Great work