I was able to discover the problem.
It appears that the Gravity Forms add-on has its own validation which does not check the status of validation prior to perform its own logic. Therefore, any previous validation that had failed would not trip the Gravity Forms validation, therefore allowing Gravity Forms to validate and removing them from the product page.
The solution to this is to add the following code to line 414 of the gravityforms-product-addons.php file:
// If valid is passed in as false, do not complete validation
if(!$valid)
return false;
I have submitted this as a bug, so hopefully it will be resolved in a future update.