I have recently just switched from Firewire 800 to Thunderbolt II using Apollo Duo. Running Cubase 9.01 when loading my template with VEP Pro 6 or internal VST Instruments hosted in Cubase or VST Rack with VEP 6, I found an issue where Midi or connectivity does not send data to the VST instruments or VST Rack instruments. I have tested by loading Knotakt as a VST Insturment as I thought it was an issue with sending data (MIDI) to VEP Pro, but found that it doesn’t even initiate the loaded instrument in Kontakt and loading a sample like Spitfire or Berlin VST, Kontakt does not detect a connected VST Bridge so the Instrument does not connect.
Now midi is working as you can see midi data transmitting from the MIDI keyboard and the channel also indicates MIDI activity. But the VST Rack or Instrument does not indicate MIDI activity. Looking in VEP 6 there is also no activity either.
Further Testing, I do own Studio One Pro version 3.3 and I loaded my template in Studio one, and everything loads just fine and connects to my instruments and everything plays correctly every time without issue. I cant explain it. If I run studio one and then shut it down, and then load Cubase 9 it will sometimes resolve the issue. But its not all the time and I am at a lose. When using Firewire 800 out of the Apollo, there was no issue. So I am not sure if I am missing something but I think there is a bug. Please let me know what you need in order for me to assist you.