It is difficult to see enough detail in your pictures but it may be something to do with Automation being turned on accidentally. It is not possible to see the Automation controls on your Multitrack view because the tracks aren't tall enough to show them. But if you make the tracks taller so that you can see more you can then go to the Automation bar where it says Read and change that to Off.
Normally unless some Automation has been recorded on purpose having the setting on Read shouldn't matter. You could try and start a new session insert some of your files onto tracks and save to see if a brand new session works OK.
Our expert on session files is SuiteSpot. So if you are lucky and he sees this thread, and you ask nicely, he might be kind enough to ask you to send him your .sesx file for analysis which might show up the problem.