I’ve been without my MeeBlip over a year, but used to sequence it with the MD. I do remember issues. I don’t remember specifics or solutions. That was also with an early MeeBlip firmware without CC control. I really liked it’s sound (and miss it). I didn’t like when they cleaned up the OSC and messed with mix and PWM from the earlier firmware. I was forced to learn how to mess with the code to implement CCs or use the newer firmware, and I did not like the sound or controls. So, I ditched it. If I recall correctly, I was looking at a midi filter to sequence it from an elektron box while still sending what I needed for other synths 
