There are 2 types of midi ports, ALSA and JACK. JACK1 contains an internal client to bridge between them, while JACK2 needs an external utility. Personally I have no clue how well this works as I don't use midi..
Hopefully reaper will get support for ALSA midi too some day soon.
What to do if it's glitchy is something I really can't advice on. Maybe try to troubleshoot it well and post here. I think control surface support is something very much untested in reaper for linux.
Edit: Yes the suggestion to try 3 periods / buffer, bigger bufferzise, etc is probably a good one. Also possibly to make sure that you've raised the priority of the soundcard interrupt if you haven't done that already.
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Reaper for Linux Documentation (WIP). Software: Archlinux/KDE, Fabfilter FX, Komplete 8, Nebula, Schwa/Stillwell, T-racks Max/Amplitube/SVX, etc. Gear: i7-2600k/4700HQ/16GB, RME Multiface/Babyface, Behringer X32, Genelec 8040, etc. :)
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