SilverBlueMedallion
but now this breaks other things. Seriously, seems like Cakewalk still has a lot of MIDI issues to sort out.
You need to be specific about what "breaks." Also, what happens if you select searchback but not zero controllers? Are you clear about how continuous controllers aren't always continuous, in the sense that sending one value will cause that value to be retained until there's another value sent? This is why when you said "to add one more piece of information - while one of those tracks is playing out of key - if I hilight that track and just move the pitch wheel a bit and then let it go back to the center, it then plays the correct pitch!" it's really expected behavior...SONAR is reacting to a previous pitch bend message, and in this case, you're giving SONAR a new one that's what you wanted.
It seems that perhaps the problems you're experiencing may not involve SONAR, but stem from a lack of understanding about how MIDI works. If that's the case, you're looking for problems in the wrong place. Functions like zeroing controllers and searchback are common, so someone versed in MIDI would look at the status of those functions first if experiencing a project not following previous controller settings. If you can be more specific about what "breaks," perhaps we can sort this out for you.