Symptoms

Everyday, the first PDF create renders in an unreadable and improper way by being highly compressed to the left. All subsequent PDFs render fine.
 

Diagnoses

After much investigation it was discovered that if the form were set to anonymous access and therefore did not have to pass through Windows STS before loading up the form then the form would render appropriately.
 

Resolution

As a workaround the form was set anonymous access enabled. Additionally setting the PDF Converter service object to use serializedResources and not webKit worked in testing.