I'm running into this same problem. When I try to play the stock sequences from the TB-3, the Microbrute stops responding, a note gets stuck on, and I verified that the midi receive channel has changed, just as you explain.
There are a number of videos on youtube showing people running sequences from the TB3 to the Microbrute -- so I guess they are just avoiding slides? Or, might this have anything to do with the firmware version on the TB3? Maybe those videos are using old firmware before the CC102 issue was implemented? The firmware 1.1 update notes do mention CC102 mapped to slide.
It's too bad this pairing doesn't work anymore.