I have two different models of iOptron Mounts that I run in remote observatories without any issues, One is a non-EC encoder and the other is enhanced. Both mounts do not use the hand controller connected to the mounts.
Dale is correct that the firmware installed in the iOptron mount must be the correct version (mount firmware matched to Commander) for Commander to function properly. Though firmware and Commander don’t seem to be the problem here.
Another is to remove the hand controller from the mount and connect the mount directly to the computer. Ensures prevention of any potential communication issues. I had this discussion with iOptron support staff a few years ago when T-shooting a com problem on my older mount where I updated the firmware in it. FYI you do need the hand controller to upgrade the mounts firmware and the hand controller at the same time. Remove the hand controller after the update.
A tip I found useful when setting up a NINA sequence for the night. When all the apps are loaded, i.e. Commander, use the mounts Zero function in Commander to zero the mount. If for any reason you think the zero position changed use the Search Zero Position. Monitor the mount as it moves. It should move some distance and return back to the zero position.
Next, from the correct zero position set the mounts Park position to where you want it and save it through Commander. Now when NINA is connected you should have full control of the mount and when the image session is completed it sholld park the mount to your desired location all without a hand controller installed.
Another thought is to make sure ASCOM is updated to the latest version and any drivers needing update. I found I had to update my ASCOM to the latest when I updated NINA to the latest build. Now everything is running smoothly.
Last, Taking the suggestion from a previous poster, it would be a good idea to contact iOptron Support and hear what they may suggest,