In the Options dialog's Naming Scripts section, there are two types of checkmarks, with two different functions. 

(#0) This checkmark apparently means: are ANY scripts ALLOWED to run?

(#1)  The checkmark next to each script looks like it means the same:

• "enable/disable this script from being allowed to run", 
•  for example, "is this allowed to be shown in the context menu when you right-click a track in the main screen?"

but this checkmark actually means

• "Should I run this automatically on all files without prompting?"

Suggested fix is quite easy: 

• add the words "Run automatically?" above the checkmarks.

• (Bonus) add the word "Enable" next to checkmark #0, as in "Enable tagger scripts".