Hi Jeff,
Hmmm...taking a look at the source code, it looks like the canonical header tag is being added in by the System SEF Plugin in Joomla.
There have been some modifications to that file between Joomla 3.3.6 and Joomla 3.4 so those are likely the cause of the new behavior:
https://github.com/joomla/joomla-cms/commits/staging/plugins/system/sef/sef.php
I'm wondering if @Hackwar might have some quick suggestions?