Hi Blaine, i'm an avid Ctrlr user at the moment. mainly making silly UI things, trying to learn Lua, sort of getting the hang of it. - don't know if you want to share the Ctrlr panel file ? i'm on 64-bit.
i think i've got my head round 2 way communication, but haven't implemented it yet in my own project.
maybe try making a cut-down VST plugin, only a few parameters, and see what happens. if your plugin is receiving some kind of intialize or something from the DAW when it starts? if it works as a standalone then you should be on the right track. is it using sysex or midiCC/NRPN? Dom