Quick reference default - reference product display from commerce product type gone

I have just upgraded to commerce 7.15 and Drupal 7.20 and have noticed the following issue when trying to set the default product display type to my commerce product - the quick reference default collapsible block is no longer present (see screenshots before and after) - /admin/commerce/products/types/product.

I have an old version of the site running on 7.15 and commerce 7.x-1.3 which does have the functionality present (not sure at which point I lost it).

I have approx 16 product content types - a simple original one with standard fields that is for products that do not have attributes so therefore 1 to 1 relationship commerce product to product display, all the other templates are for various attribute driven products that have different fields e.g. colour, length, grade, height etc etc. This has all been working well and I have been using commerce feeds + tamper to import approx 10,000 products of various types.

Today I went to create a new product manually and noticed that when choosing the standard product display from content > add content > product display (also using inline entity form 7.x-1.1) when I go to create the commerce product from within the inline entity form it is not showing me the standard commerce product type but one of my custom commerce products with additional fields instead. As the quick reference default option has disappeared I cannot check and rest the relationship between my product display and my commerce product.

I am using an omega responsive sub theme and also have a multisite attached which uses its own database but shares the same codebase.

Also using many contrib modules but very little template customisation. My modules are mostly up-to-date with only a few out of date. Unfortunately I cant display a link as its on our dev box and firewalled. Included contribs (not extensive):

• inline entiy form
• commerce UPS
• commerce extras
• postal code filter
• sagepay direct
• commerce Checkout Progress
• Commerce Extra Price Formatters
• Commerce fancy attributes
• Commerce Search API
• Commerce Wishlist
• Physical Product
• Product Attributes
• Database search
• Search facets
• Search views

I have to say I'm majorly impressed with where commerce is right now and the number of contrib modules now available...

Due to go live in 3 days so any help appreciated!

EDIT:
I have tried commerce repair...