Hi, I own a first generation Tacx Neo. I do have an issue with the gearing/ indexing. It used to be fine but suddenly the gears are all over the place. I changed my chain and cassette( this one was three years old by now) but still the problem. I took it out of the trainer and indexed the gears again with the normal wheel in. Then when I put it on the trainer, same problem. What is wrong? Any suggestions are welcome
Have you checked the tightness of the freehub on the spindle? Would be a good idea to grease the spindle as well
Something will most likely cause a horizontal offset of the relative position between trainer cassette and frame and wheel cassette and frame.
In addition to the freehub, I would check that the frame is properly positioned on the axle and that it is not tilted, that any required spacers are in place and that the quick release is really tight. (or at least the same tightness you use when the wheel is in place)
Tacx Neo 1 owner here. I can only attest that all of the above suggestions have been issues for me in the past when I had: increased noise levels, gear changing issues or vibration problems.
So like Jonnyboy and tigloo said: make sure everything is tight, in the right place and level 
I had an increase in noise and found the cassette had worked itself loose. I tightened it up and it helped but then starting having freehub issue where back pedals were not smooth. However as long as the hub is engaged and pedaling under load there wasn’t a problem.
I took the cassette and freehub off and cleaned it all. It’s been about a year since I bought it and the grease was all pretty black on the axle and freehub pieces. I relubed and put back together but still had the freehub issues. As you tighten the end cap nut (not the cassette lock ring but the separate nut that goes over it) it makes the problem worse.
I contacted Tacx and am waiting to hear back but I’m pretty certain my freehub needs replacing. Perhaps it was damaged with my cassette becoming loose, or perhaps it just failed. Not certain but hopefully a replacement freehub fixes the issue.