I've had issues with power cycling Vera with the USB gateway connected, what you need to do is unplug the USB gateway and power on Vera, wait for it to fully boot and the Lua engine to fully load, plug the gateway in, then go into settings -> Z-Wave -> Advanced and click on "reload engine" (why this is here when it has nothing to do with z-wave is anyone's guess), then refresh your browser and it should show up in serial port config (assuming it's a genuine FTDI). You'll need to do this EVERY time you power cycle vera in the future... or at least that's my experience with Vera 3 on UI7.

I've read somewhere a while ago it's somehow linked to the startup power draw on the USB port and using a powered USB hub will fix this but haven't had the opportunity to try

I had the same error and it turned out that for some reason it was finding the library in a folder in My Documents and also in the Arduino install folder. I renamed the copy in My Documents (I don't remember putting it there so maybe it was older version?) and all was well.