There's a pretty ridiculous error in the flatrate module. The primary key for the uc_flatrate_products table only allows for one entry per node revision. In addition, the hook_nodeapi() deletes all of a revision's entries when it saves each adjustment. This means you can only have product-specific shipping rates for the last method in the list. And for everyone who upgrades from alpha8, that method is the flat rate per order. Not helpful.

I've fixed all this in the latest code. As a temporary fix, you can delete all but one of your flat rate shipping methods.