It sounds as though you have reversed the field order of your video. AVCHD is always upper field first (if it is not progressive). Encore may have reversed this to make your MPEG-DVD files LFF.
If your original footage was shot as progressive, a lot of AVCHD is actually saved as PsF - this has two identical fields, and Premiere tends to see it as interlaced. If you did shoot progressive, then you need to use the Interpret Footage command on your files to tell Premiere that they are Progressive.
