I've been struggling with this problem since I wrote this post originally. I came up with a solution, basically to rearrange my scripts so that the CC reception was in its own script. It had been in the main interface script, since the CC's were controlling scriptSliders that were attached to module attributes. I moved the CC receive functions to their own script, and used setAttribute to target the sliders in the main interface script. Just chiming in here to let anyone that comes across this know how the problem was solved.
Now I have some other problems. It seems impossible to set a AU/VST parameter directly from the script by this method. Sending a value to the linked scriptSlider causes a change to it, and it's linked attribute, but doesn't change the VST/AU parameter value in the host. I'll make a separate post for that problem, though.