Hi Welcome just answer.
Does the system play any disk? Have you taken the cover off to look on the cd loading mechanism? This is the first thing I would suggest to look at before any thing else. Take the cover off and observe the system operation and let me know if you anything unsual. Some of failure I have seen before are related to miss alignment of the loading and counting mechanism.
Have you tried to clean the mechanism that rotates the discs. Power off the system before performing the cleaning.
I am starting to think the sensor is not finding position correctly. I am probably think, you may want clean the internal mechanism and visually looknow for debree or any pieces inside the system.
Dust is what can cause these errors. Just blow any dust you might seek on the inside.
Thank, pay attention to see if the cd carrier can move to a different position when power is off.
OK so the system is mechanically sound. I have looked at Sony website and they do not have a firmware for this. My only other suggestion is to contact Sony for repairs. The system uses micro controller which is similar to a computer. The system will need to be programmed externally using Sony proprietary hardware and software.
I would think that the sensor has to do with what you are seeing. If you remember, I mention about checking the sensor and removing any dust. The sensor uses optics to count CD positions. If the sensor does not know what number the cd is, then it will not count right. At the same time, depending on the system, there might be a second sensor to correct the first one. If one of these fail, the accuracy of the position will never be correct.