The only time the Order Importer will use the Shipping Rule selected when you configured a profile, is when you explicitly configure it to also dispatch the order as you are importing.

Orders that the Order Importer loads into the Dispatch Queue for picking can not be assigned a specific Shipping Rule and should always behave like an ordinary order coming in from any other channel.

Thus, in general, you should first look at the configuration of your shipping rules to check that they include the channel you are importing to if you are experiencing issues with it being picked up by specific shipping rules after triggering a recalculation.