If a query with substitution variables has comments in between the queries, the Editor will not prompt users for substitution variables even if View | TOAD Options | Execute/Compile | Prompt for substitution variables is CHECKED.
Possibly, the formatter in TOAD 188.8.131.52 doesn't recognize comments in a code when executing a query as a statement (F9.)
Remove the comments from your query or Use F5 (execute as script) to run your query.
Issue fixed in version 184.108.40.206. The latest version of Toad for Oracle can be downloaded here.