Hi,
Ah yes, I see what you're talking about.
We've added a few releases ago the possibility to restrict custom fields of the "order" table based on the selected shipping and payment method.
This means that when the shipping method or payment method changes, we need to refresh the custom fields area.
If you don't want/need that, you'll want to edit the file checkout / show_block_fields.php via the menu Display>Views and change the line:
window.Oby.registerAjax(['checkout.fields.updated','cart.updated','checkout.shipping.changed','checkout.payment.changed'], function(params){
to:
window.Oby.registerAjax(['checkout.fields.updated','cart.updated'], function(params){
Another solution would be to move the fields and the shipping/payment selection views on different steps, or to place the fields view after the payment/shipping views so that the customer enters his data after selecting the shipping/payment method.