I had the same Problem in Cubase.
You have to turn off the MIDI control from Windows. I dont know if its the same problem, but in Windows 7 you had to turn off the MIDI Control for the SubPhatty in the audio preferences.
That your DAW is the Master. Then i used MIDI & USB. MIDI to control notes etc. and the USB to control the VST.
Its Pain in the ass.
Now I try to control the SubPhatty via CV but i dont get it to work 
Bought a Sub Phatty a couple of weeks ago. It keeps disconnecting from usb. The Editor can’t see the synth and it says hardware disconnected.
Ableton is crashing a lot when using the vst editor.
Can’t believe this is still a problem… this thread is from 2014, now is june 2017. I’m really disappointed. I thought Moog had a name for quality.
I don’t have these issues (I also don’t use Live), but there is a new editor and firmware in beta now. If you’d like to check if your issues are fixed in the new version you could join the beta testing group as explained here: https://forum.moogmusic.com/viewtopic.php?f=21&t=25663
Ehem… so, checking back here again, after two years. Still no new firmware or software for the Sub Phatty to fix usb-related problems, and no info in the beta-testing post. Could any of the beta testers please provide some info, a status update, anything? Will a working solution ever be released? 