Not really sure why things are acting odd, but maybe changing your method could help
Since you are exporting so you can import to another session, instead of the extra steps to export, followed by import, why not skip the export step, open the session that you want to bring the midi in, and use the Import Session Data function and import the midi(or instrument) track directly from the source session?
Remember that when you export midi, it exports ALL midi in the session(I'm not even sure if its possible to only export some). Using the above suggestion allows you to be more selective on what midi you bring into your new session. Re the old bit of Pro Tools sucking at midi, that's really no longer the case. While it may not be as slick as Logic or "insert DAW name here", its still miles better than it was a few versions back(and it gets better with each major release).