So, up until 11 I could right click on something like $this->load->view, $this->model, etc using CodeIgniter framework when I had my phpdoc loaded and it would find it - now in 11 it returns cannot find variable.

Has anybody else ran into this problem with CI style setups?

From what you posted I see only $this variable. IDE normally can find it easily as it is pointing to the class where you placed the variable.
As of properties like load, model, and view -- it depends on how they are declared, if they are declared at all. From these perspectives, v11 does not change anything toward CI. If something worked in previous versions, it still works in v11 too, otherwise you may want to report it to support and provide more details on the problem.

I've noticed that the additional directories property in project properties gets cleared, stopping code insight working for my Zend projects.

Might not be what is happening to you but worth a look.

I have the same or a similar problem with autocomplete in Version 11.
I use Yii Framework and include files are not uploaded yet that Yii framework is a directory with the framework added to your project .
Appears only in the tab Run & Debug - . > Run target - > Maping for debugger. The Code insignt - > includes not .
Can not work for Code Insight framework. Quite important thing PHPEd for me in this state unusable.

Now It's OK. Was deleting a project created in version 10 and re-create for Version 11.

The framework directory is picked from the setting of the Php Framework tab. If this directory is also found in Addtional Directories, PhpED removes it from here. So the behaviour is correct.
Regarding code completion -- before doing anything, just check if Code Explorer tab lists the classes/functions/variables/properties etc you're expected to see in Code completion dropdown or in Find declaration. If you do not see them there, check if corresponding directory with sources is either in the project, or in Additional directory or pointed in the Php Framework, then try to refresh Code Explorer If nothing helps, contact support.