Hello,
For your first question, reaper tries to know the latency of your sound card and shift your recording so if you heard it in time but it was actually not, it would be fixed when you play. Please keep in mind it's my understanding in accordance to certain preferences options and might be wrong.
Use wasapi for your sound system, it has the lowest latency of all others if your sound card doesn't support ASIO, set the priority to time critical and set the block size to 250 or lower, it'll use more of your CPU but the latency will be lowered significantly.
For your second question, all the midi tracks that are armd will be played when you play midi, so be sure only the midi tracks you want to play/record are armd. If this is not the issue, check that the midi track is not sending to your other tracks using track routing. If you find something like, send to track 2. Delete button, it's sending to your other track. You can delete it or add new send/receives here. I don't quite remember but there maybe an option that makes new tracks send to all of the others. check the track/send defaults in preferences.
GOOD DAY.