Sorry I was testing on an older version that was using version 1 of the project system.
I have the same result as you describe, so there is something wrong. After looking at the generated project file, there is an error where semicolon are used instead of comas. There is already an issue on github
setup_new_project generates incorrect syntax that also raises other issues, so have a look at that.
Near the end, you can change
| fkey_command = {
.F1 = "run";
.F2 = "run";
};
|
to
| fkey_command = {
.F1 = "build",
.F2 = "run",
};
|