I have script that does a lot of other thing, but one of the first things it does is run a diffrent script that set 5 variables using the Set Variable command. This works fine on it's own, but when the variable script is called from inside a diffrent script, it skips all set variable steps.

Do the all set variable steps have to be wihtin the main script?

$ variables exist within a script. $$ variables persist.

See here.

Variables

You could pass the values of the variables via a script parameter to your subscript or use global variables which will retain their values for that particular file.

Set Variable does work as a subscript, but if the variables are of the $ variety, they will be local to each subscripts. Try using two $$ for the variables to declare them as global to the file.

I did try using "$$" but the script still skipped all Set Variables steps. I witnessed using the Script Debugger

Is the context correct when the subscript is performed ?

Yes, if I run the script alone it works fine

Maybe you can post an example file illustrating the problem, or at least screenshots of the scripts.