Do you have a deck you can try and digitize from?
Try sending it audio from any other source other than the console to see if it works there.
It sounds like you have everything set up correctly to me. You might want to send a blackburst or composite reference from the switcher to the ref in if possible. Check for the newest firmware and drivers. Also, you should try uninstalling and reinstalling the latest drivers. If none of this works, I’d call AJA and see what they say, you might have a bum box. If that is the case they will send you an advanced replacement right away. Good guys/gals over at the AJA camp.
You have powercycled the ioLA I take it?
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G5 Dual 2Ghz <> 4GB RAM <> FCP 5.02 <> Kona 2
ATTO 42XS <> Huge Systems 4105 Fibre