All taxonomy populated show up even after removed

I am trying to pull in my document categories (Document Library Pro) as check boxes using the doc_categories taxonomy. I believe I have everything setup properly as my doc_categories all pull in properly and when I submit a file with them selected, it works properly and assigns the doc_categories properly.

The problem comes in when I want to remove some of the categories so the user cannot select them. I am planning on having a form for each department so I can only allow them to assign their department’s categories to files they upload.

When I remove the choices from the list, it shows properly in the edit field and on the form when designing, but once I save the form and on the page all the categories show up (as if I never removed any from the choices).

Steps:
Create a form with check boxes
Click “Advanced” and check “Populate with Taxonomy”
Save the form
Click on the check boxes, go to the right under “General”
Find the list of choices pulled in from Taxonomy and remove the ones I don’t want to use
Set the values to the correct values (seem to have not pulled in the correct ones) and save the form.
When I save the form, the categories show incorrectly on the preview of the form
When I look at the website, it shows every category (even the ones I removed)