Flat Rate adds rates i don't want to be added

I'm using Commerce Shipping 7.x-2.0 and Commerce Flat Rate. We have a online Shop and everything is properly set up. But theres one random thing i didn't set up: I have a shipping Rate of CHF 5.00, which is added to the total amount once. But Shipping adds costs of 1.50 CHF to every line item, and i cannot change this. Not in the Code and not in the UI. Can anyone help me? For further Information, just contact me...