Previously we had discussed that the layout file you sent had the track segments with color set to non-white. This explained how it looked. I had assumed that came from an older parameter file and then you tried the Beta 1 version but it had lowercase "a"s - so I sent you a copy of the Beta 2 copy.
So we need to reset my understanding.
1. On Beta2, did you ensure the parameter file you are using is the Beta2 one? Check its filepath is correctly pointing to the Beta2, if not reload.
2. Did you delete the existing copy and re-insert the beta2 version?
3. Did you Save?
4. Then did you Start?
Is no other version running on the same layout...
I should explain that if you didn't explicitly Save, it is possible that you are resuming with the previous version... And obviously if two copies of the program are running...
Meanwhile I will try to put the Beta 2 version into a new file, save and restart, to see if there is any problem with Save/Load....