Kyprianos,
Your observation of the Accuracy Index is correct. I found I had the same result as it went to 9 after thirty minutes of flight.
I added the update flags gauge, to check dme and both green flags appeared by pressing the test button. It didn't make a difference having it.

gauge05=../Civa/Ins!UpdateFlags,  130,0,100,70

I loaded both CDU's with duplicate waypoints. I went back and forth between Seattle Ksea and Bowerman Khqm. After thirty minutes I had to change waypoint, insert twice to get the correct heading established.
I noticed there was a 0.5NM difference between cdu1 and cdu2. I never had any action or malfunction codes.
I followed the Operations Manual Chapter 4: Normal Procedures.
I'll search over at simufly.com and look for an answer. Don