This depends on the original field order (different from field dominance) It sounds like the fields were reversed on encode so do the opposite of what you did.
You can determine what order your system is (now a days sytems are lower but there are some old systems out there that are upper) by looking at every 5th frame of a field rendeed clip. If the clip is upper and you are on a lower field sys then the fith frame will look e some action is going backwards in one of the fields.
Just make sure all field orders are the same all the way through the project. This is determined by your capture system.