Probably a tube went bad, it's time to start swapping tubes from one channel to the other until you find out which tube is the culprit. Of course you will have to swap the tubes in the power supplies too.
Ykauyeung, I have exactly the same Aesthetix Io set up that you have: dual power supplies and volume controls. Since you are sure the issue does not arise playing CD through the AUX input, then I agree you have isolated it to the phono stage. Here is what I would do next to identify if you have a problem tube...
The phono stage is comprised of the first two gain stages. Each gain stage has two 12AX7 tubes. Start with the first gain stage and swap the two tubes (labeled V1 and V2) to the other channel. If the problem changed channels, then it is one of those two tubes you just swapped to that channel. Swap one of those tubes back to it's original location. If the problem changed channels again, that's the tube that needs to be replaced.
If the initial swap of tubes did not result in the problem changing channels, go the the second gain stage and swap the two tubes in the second gain stage. Follow the same steps as above.
This will give you the least number of on/off cycles for diagnosing the problem.
"In addition, how you use the Aux input at the IO? the CD or second cartridge."The Aux input can only be used as a high level input. It does not pass the signal to the phono stage so it cannot be used for a second cartridge (unless the second cartridge has its own phono stage outside of the Io and you're passing the output of that other phono stage to the Aux input). I use the Aux input for CD or Tuner, changing the cable at the source end depending on which I want to listen to.
Good luck diagnosing your problem. If changing the tubes does not isolate a bad tube that, when replaced, solves the issue, you should call the factory for advice from Glenn or Jim.