Sorry to bring up an old thread, but I was actually checking out a MCU from Craigslist and initially ran into this same issue with the MCU causing the first track to arm record on and off. After looking up the manual for it, I found out that there's 3 different modes the MCU can be in - Mackie Control, Logic Control, and HUI. For Reaper, you want it in Mackie Control mode.
Taken from the manual:
https://www.manualslib.com/manual/69...?page=3#manual
To change the mode of operation:
1. Turn off the Mackie Control.
2. Hold down both the Ch. 1 and Ch. 2 SELECT buttons while turning on the Mackie Control.
3. The display once again prompts you to select a mode of operation
Press Ch. 1 V-Pot to select Mackie Control.
Press Ch. 4 V-Pot to select HUI.
Press Ch. 8 V-Pot to select Logic Control
So all in all, you want to change the mode of operation to Mackie Control for use in Reaper. I was able to do this and get it working with my computer, and now I have a $150 Mackie Control Universal