Not sure if this info helps. But mapping a button on my other controller apc40 mkII to a problem clip with the clock running off the mpd 232 at the same time works fine.
If I configure a drum pad to send out the same note as that button I mapped on the apc40 and then try to use that drum pad instead the problem starts to happen. I'm not really sure what it hates about the mpd..
I've open R5 to see if the mpd is still ok and it's working fine there still using the same old comp I made in R5. ><
edit recorded a little video to help demo the experience https://youtu.be/vWv4L4RKkBU
All I'm doing in this video is showing that after starting the clock on the mpd if I change clips then hit the drum pad assigned to that one solid that flashes the output monitor every beat it causes the clock to go crazy. I have to change clips in the comp first to make it happen every time I touch the drum pad. If I replicate it via the apc or even my touch screen it doesn't happen. Only when sending notes off the mpd.