Scaling down & up in CS5 - quality loss?

I have a bunch of source videos in various formats and dimensions, all of which I'm scaling down to 480x360. Here's my dilemma:
Because the source resolutions vary (they're all larger than 480x360 though), I've found it easiest to use the Scale to Frame Size function in my sequence. However, occasionally after doing this there's dead space along the borders that I'd like to get rid of - in this case the easiest route is to then scale up the clip a percentage or two via the Motion effect.
What I'm wondering is, is this scaling up in Motion referencing from the "Scale to Frame Size" resolution (thereby resulting in a quality loss, as I'm essentially shrinking the source then blowing that smaller resolution up slightly), or does it remember the original source dimensions and adjust from there (in the final equation then just scaling down "not as much")? Does that make sense?
I can always not use Scale to Frame Size and scale down solely from the Motion effect, but this requires trial and error to figure out exactly how much each source needs to be scaled down. As I have many files to work with, the time spent doing that adds up quickly...

What I'm wondering is, is this scaling up in Motion referencing from the "Scale to Frame Size" resolution (thereby resulting in a quality loss, as I'm essentially shrinking the source then blowing that smaller resolution up slightly)
Correct. It's a scale down to fit before the Motion:Scale parameter, so adjusting that parameter above 100% will introduce quality loss.
I can always not use Scale to Frame Size and scale down solely from the Motion effect, but this requires trial and error to figure out exactly how much each source needs to be scaled down. As I have many files to work with, the time spent doing that adds up quickly...
That's your best bet. Scale to Frame Size is, in most cases (and in my opinion) almost totally worthless. It used to function "correctly" in that it would actually change the Motion:Scale parameter, but that changed a long time ago.
If your photos are of all radically different sizes, you're probably better off scaling in batches in Photoshop (Actions, for example). If you've got a smaller set of varying sizes, I'd just create some effect presets for the Motion effect that set the proper scale for each of the various dimensions. It shouldn't take too long to set up.

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