PHP Code Filter & Themed Field Collections

Just wondering if anyone can shed some light on an issue I'm having.

I'm trying to output a view within a field collection using views_embed_view(); and the PHP Filter in conjunction with a Textarea field.

I have used a template file to theme the output of my field collection and for some reason I cannot get the PHP to execute properly within the output of the field.

Doing a DPM on the field I can see that the php format is applied and that the text in the field is being stored properly.

However when I look at the source I see it gets commented out. I currently have disabled the CKEditor as I figured it may be related some how but I can only narrow this down into the theming of the field collection.

*** I should note that this exact code works fine within the main body field on my page. I've also replaced the print statement with a return render(); and have had no luck with any sort of rendering on this field.

Thanks in advanced!