I believe this change in behaviour was introduced in v1.6.3 (or newer) and is still present in 1.6.4b1.
A form has one or more products. These products have 'product options' associated with them in the form of check boxes. Ticking these product options will enable various other products to be displayed.
For example, [product 1] has an option [product 1 option], using conditional logic, when you tick [product 1 option] then [product 2] is enabled (conditional logic is setup in product 2).
In the form, after enabling and selecting the second product, the total price is updated accordingly (showing the sum of product 1 and 2). However, upon submission, only product 1 is submitted and the total price only shows the total for product 1 (product 2 was not submitted at all).
In previous versions of Gravityforms (I believe before 1.6.3) this functionality worked fine and both products were shown after submission.
For basic scenarios it is possible to replace the product options with generic check boxes. Doing this, both products are submitted as expected.
For more advanced cases, where the product options perform additional functionality related to the product, it is not as simple to work around this.
I was able to duplicate this on multiple forms and with multiple versions of gravityforms. The products were of type dropdown. I am uncertain whether this is a factor. For my current use, I have been able to workaround the problem however I still thought it was appropraite to report this behaviour here.