I don't know the first thing about Thunar, hence I have no idea what %F or %D may represent in this context, but:
...will move
foo to
bar. If both are directories, the former will end up as a subdirectory of the latter. However:
...will move all items (files and subdirectories) in
foo to
bar, but the directory itself (
foo) will not be moved.
In other words, you may want to add
/* to the parameter representing the source directory.