If you change your shipping cost settings in Escalafy — for example, from custom shipping (manual estimate) to "order shipping cost" — past orders that already had $0 shipping cost recorded will keep showing $0. The change only applies to new orders that come in from that moment on.
Why don't past orders change?
Once an order has a shipping cost recorded (even if it's $0), that value is locked. If the original order cost didn't break out the shipping charge, Escalafy can't make that data up retroactively.
New orders, on the other hand, are created with the updated settings and will reflect the correct shipping cost from the start.
Recommendation
Change the settings going forward, but don't try to reprocess the history of orders that never had the shipping cost broken out. Doing so won't add data that wasn't in the original order, and it can create inconsistencies in your reports.
Seeing an abrupt change in shipping costs from a certain date? That's expected. It marks the moment you updated the settings. The earlier figures are correct for the period they covered.