Compressor 3.5.3 won't letterbox or remember saved Padding settings

I'm taking a screen capture out of ScreenFlow into Compressor 3.5.3 and I cannot get it to letterbox to 16 x 9. I'm not new to Compressor and have tried everything I can think of and done numerous searches searches with no success.
-Original Pro Res 422 file is at 1600x1000
-Inspector/Geometry tab is set to: Cropping- Custom, Dimensions- 640x360 Custom 16x9, Padding- Custom
(I've tried many times, but the Padding setting of 16x9 won't stay. I hit "Save", click on another preset, come back and it's returned to "Custom". This is likely connected to the problem, but re-booting the program doesn't help).
-Inspector/Filters tab: Letterbox- Type: Matte or Scale (neither works), Position- Center, Output- 16x9
(This doesn't work either. The settings do get saved, but no letterboxing.)
-Inspector/Encoding tab: Use x264 encoder.
Am I missing something simple and obvious? I can easily export from QuickTime 7 or even from ScreenFlow directly and it works as it should. The reason I choose Compressor is simply to save my settings as a preset since they aren't retained in QT 7 when I create a different type of export.
I don't have to use Compressor. In theory, it's just to save me time, but after an hour and a half, it's faster just to jot down my settings and then re-input them into QT 7 to export with letterboxing.
Thanks,
Dave

Russ,
I switched the Padding setting back to: "Preserve source aspect ratio" and it worked this time. It was probably the first thing I tried without success, but it's fine now.
I did notice that after numerous export tests that the final quality when viewed in Quicktime was slightly different when I used the padding vs. having the padding and Filter Letterbox settings both on. Oddly enough, it seemed a bit better when using both. This could just be a bit of randomness in that every single export will be of slightly different quality, but it is easy to see a difference when you take an exported screen capture at 640x360 and view in full screen mode. Anyway, I guess it's all working now.
Thanks,
Dave
P.S. I'll check back on this thread later in case you have anything to add.

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