Hi Chris,
We released v5.1 to address the changes in SharePoint 2013. You'll want to download v5.1 and use it to reinject qRules into your forms. First, open the forms with InfoPath 2013 Designer and save them as 2013 forms. Then, run the qRules injector.
SharePoint 2013 is a huge change. We've been grappling with it. Office 365 multiple tenancy sites are all running the latest sandbox and qRules works as expected there, but SharePoint 2013 standalone still has some bug and qRules' SaveToSharePoint command doesn't work in sandbox (you will have to admin deploy if you use this command).
If you were able to publish for 2010 (as site collection admin), you should be able to re-inject qRules and publish to 2013. The only major gap right now is SaveToSharePoint and that's for standalone ShP only - O365 works just fine.
Hopefully, this explains something ...