You purchase a WordPress Toolkit Deluxe license for a single account. Only a single account appears as enabled on the WordPress Toolkit page in WHM, but a warning like this displays at the top of the page:
License overuse detected: WordPress Toolkit license allows 1 Deluxe accounts, but 2 Deluxe accounts were assigned. As a result of this overuse, WordPress Toolkit Deluxe is temporarily unavailable to all accounts on the server. You can either upgrade your WordPress Toolkit license to accommodate more accounts, or unassign WPT Deluxe from certain accounts.
This warning appears when multiple accounts on the server use a package whose feature list has WordPress Toolkit Deluxe enabled.
Either upgrade your WordPress Toolkit Deluxe license to accommodate multiple accounts or create a new package and feature list for WordPress Toolkit Deluxe, and assign only the account for which you want to use WordPress Toolkit to that package.