In AME, in the upper left hand corner of the Media Encoder Pane, set the drop down menu Source Scaling to Stretch to Fill.
Does that help?
Good thought! I tried it but doesn't work. In this case my "source size" and "output size" are the same since my sequence and output resolution is 1080p. So stretching/scaling etc doesn't actually change anything.
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You need to go through all your PAL footage in the project, right click (on PC), and choose Modify-->Interpret Footage.
Under Pixel Aspect Ratio, you will see selected "Use Pixel Aspect Ratio from File" and then the correct setting D1/DV PAL (1.0940)
However, you need instead to check the box "Conform to:" and then choose D1/DV PAL (1.0940).
This will force the encoder to use the D1/DV PAL standard, and not give you the square pixels.
Apparently the encoder has difficulty reading the file's Pixel Aspect Ratio, and substitutes the default setting of "square pixels,"
You totally just saved me.
I couldn't figure out why Encoder was not interpreting my footage correctly, but my export from Premiere was fine. I tried your suggestion and it worked!