Strange behavior when comment_alter_taxonomy module is enabled after node is already created

I first mentioned this bug in #311480: Refactor and simplify the comment form workflow but decided to commit that patch and tackle this bug in a new issue.

Disable cat. Create a new issue, and assign some terms to it.
Create 2 or 3 comments on this issue.
Enable cat, but don't enable cat for any vocabularies.
Create another follow up on the issue.
Enable cat for all the vocabularies you used in the first step.
When you view the issue, the terms appear to have been removed in the first comment, and then added back later on, even though in reality you only assigned the terms on the original issue node.