So you are saying if cart has regular products, shipping cost is flat rate for whole order ...
If cart only has special shipping products use USPS and/or UPS ...
If cart is mixed, meaning it has even 1 of the special shipping products, turn off flat and only offer UPS and USPS based on the total weight of the whole cart?
Do you have anything that "distinquishes" these special shipping products from other products?
While this would require some coding ... assuming there is a way to identify the differences ... perhaps this idea work a little better ...
All products have 0 weight except those that require UPS and/or USPS
0 weight is set to mean NOT Free Shipping in the Shipping/Packaging
When 0 weight, flat runs
When not 0 weight, the Handling charge for the USPS and UPS is the same as Flat to cover those products ... and then the calculation is made on products with weight in normal fashion for UPS and USPS
If that would work ... then this could be customized to run your shipping in this manner with some custom coding for turning ON/OFF the flat, usps and ups shipping modules ...