If you make a copy of a form that has the same name but a different prefix, and then upgrade, the form is not listed as a form in the Report Builder. But it will be listed, if you go to the Form Builder.
As a temporary fix, change the label of one of those forms and it will show up. We needed to sort the form labels based on lowercase strings and the pair <label, name>, so that identical labels will still be displayed. Moving forward, an issue was resolved in the Report Builder, where forms under the same module and business object, and with the same label but different names, would not be listed. Only one of the forms with the same label would be displayed.
[Admin: This post is related to the 02.24.17 post by Rob Zombron about forms missing from Report Builder.]