My source avi (divx encoded) doesn't "look" interlaced, but when I load it in TMPGEnc (using the wizard), TMPGEnc wastes lots of time "judging field order" and then tells me it is interlaced.

Now, in cases like this, when the two fields for each frame are clearly representing the same instance in time (i.e., not separated in time as in an interlaced source), but for some insane reason are being stored as fields in the source (I guess?), should I choose "progressive" as the encode mode? Does it matter? Will it make any difference in playback quality or encoding time? Does it matter at all whether the source is field-based or frame-based, as long as the source frames "look" progressive?