Just tried this by creating two separate chains. One was saved with a unique name and the second was just saved with the project information. I changed the settings several times on both, and they reopened correctly when I closed and opened the project.
First I thought the problem might be from not saving the chain with it's own name since I noticed you had the default "fx chain" in the name field. But that didn't make a difference here.
I also tried editing the controls for a start time to be 0.00% and end to be 50.0%
I like that setting for what you're trying to do.
Sorry I couldn't repeat this for you.
<<just edited this post for grammar - wow, I can't talk with family when typing that's for sure>>