I am running some SD material through the system, and I checked the box in the MP4 delivery to force 16x9 on SD material. But it still comes out as 4x3 - at least when playing in VLC... Windows Media Player and QT don't even want to play the video, only audio
Hm, ok?
I just tried to convert an old DV 4:3 clip and it works just fine. Forcing 16:9 gives 16:9. Leaving it gives original 4:3. It plays correctly in VLC and windows media player. Premiere Pro also sees the correct aspect for both converted clips.
What are the the width and height of your source video?
Hm, that's the same SD size as my test clips. 720x576 is among the resolution criterias that tells FFAStrans it's SD material, so your clip should definitely work. I don't suppose you have a short sample to share so I can investigate further?