> but the brainvision software assumes off-to-on

correct, brainvision recorder only interprets triggering events to occur from 0V to some voltage (5V typically). This is their software implementation. it does trigger when the offset occurs for our system going from 0V back to 5V. 

>  It seems a pre or post processing step in your stream at NYU makes more sense

would you be able to correctly construct the intended trigger events post-conversion?