Checkout Attributes disappear from form if you Estimate Shipping

Also, Checkout Attribute "Attribute Values" tab allows for "Weight adjustment" (which is used by the shipping service).
Because Checkout Attributes are not posted, the Weight Adjustments are not available to "Estimate Shipping".  You must first click the Checkout button to post those fields, then you can go back to Shopping Cart and Estimate Shipping will reflect the adjusted weights.

Thanks for reporting. I've just created two work items. By "Checkout Attributes disappear" do you mean entered values are not persisted (for example, already chosen dropdownlist item)?

Yes, exactly.  When the page reloads with shipping estimate, the values that were entered in text boxes, or set in any dropdowns are no longer there.