Short answer

Well, it "works" if you change line 29 to

• $self->{SETTINGS}{thing1} = 7;

Long answer

What's happening is that you bind the references in BuildMenu()

• ['checkbutton', 'thing1', -variable => \$self->{SETTINGS}->{thing1}, ...

before initializing the values. (autovivification helps here)

But with

• $self->{SETTINGS} = { thing1 => 7 };

are you overwriting the old hash including its bound element thing1 inside, with a new hash and a different thing1 ...

I'd rather change that timing.

NB: checkbutton will toggle between 0 and 1 - those 3 and 7 are considered false like 0.