The same happens, in my case, with BoxSizers. And it does change the place controls end up in the program. (i.e. Writing wxALIGN_CENTER_VERTICAL|wxALIGN_CENTER_HORIZONTAL manually in the generated code makes it look better)
Example: I usually press the middle RadioButton on the side bar and the actual selection moves either to the top center or left center, depending on the BoxSizer Orientation.
Ubuntu, svn 10358, wx2.8.12, x64.