Hi Thomas, I have a Qnap TS 412 running just fine with Infuse on my JB ATV2 running 5.3. I can run with AFP or SMB on mine, but am currently running AFP. My only suggestion as you can run SMB shares and see your files is to go to My Files>Remote and when you see the files listed, go to each one (that does not have any media folders inside) and hold down the enter button on your silver apple remote until you see a list, then scroll down until you get to 'None", and then push menu button. Do this with every ‘non media file’. This will then isolate all files that do not need to be scanned for Metadata info. Then go to you Mulitimedia folder, click enter, and when you go to your folders such as Movies, TV Shows etc, hold down the enter button again, and select the correct meta data type - such as Movies, TV Shows that relate to the correct media file you have. This will then allow the app to correctly catalog the files for the purpose of loading correct MetaData. I trust that this will help you Thomas. Good luck!
P.S What I have noticed with the QNAP is that sometimes getting to the files using SMB or AFP can take a little while, so patience is required, Remember though that these units aren’t PC’s, and only run 1.6GHz on Intel, so they do take a bit of time to load etc., but do run quite well.