Basically I ran Terrain according to the instructions, it says to check the 'Allow Generator Overwrites' Box. Which I did. But as I am looking at the Control Tab now I see that this 'Allow Generator Overwrites' box has somehow unchecked itself.

The Allow Generator Overwrites is a toggle. Once used, it will in fact uncheck and this is normal and expected.

The reason is simple.

When you click a generator control box, one of two things will happen.

1. You do not check Allow Generator Overwrites, in which case, the software will show you what is already loaded on that generator.

2. You did check Allow Generator Overwrites, in which case, the settings that you picked will be loaded to that generator.

#1 allows you to poke and view what is running, or what would be running if the generator is stopped and you wish to start it.

You can also resume a generator that was stopped, even if you restarted the software. This would be impossible if you overwrote the generator by the use of #2, as the state the generator was last in will be lost.

#2 is only used when you want to change what is loaded on the generator.

For more details, please check the link:
https://www.spooky2.com/forums/viewtopic.php?f=83&t=9760