Been a few years since ive used Logic. Is there a VST Instrument list or panel the same way as there is in Cubase? Thats where you control your Virus Control instance and all the other VSTs, you can only open one instance of VC, then just use the MIDI ch numbers to assign parts 1-16.
Check all channel instances and make sure there is no Virus Control open for any of them (check your Midi In-Out routing to see whats going where). If the VC is already open it may just be tabbed away somewhere. Check all your windows, and dig around.
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