Add js script to register page
If you make a checkbox required it should force the user to check it (if you have an up to date version of drupal core). See the issue here where that was fixed.

For older versions of drupal there was the checkbox validate module.

As for adding javascript in your info file. That will add it to every page.
So either the page it doesn't work on is using a different theme (and therefore a different info file), or there is a javascript error on the page that is preventing your code from running.

Check your page for javascript errors.

There is also the legal module, which allows you to set terms and conditions that the user has to agree to when signing up. The module handles the checkboxes.
It might not be right for you but it is another option.