Motion Effect doesn't always work with Time Remapped clips

Hello all. I used Premiere 4 extensively (yes, '4' not 'CS4') and I'm just getting back in to it with CS6. Lots of cool new stuff to learn but I'm happy to see the basics are pretty much the same!
I'm wondering if anyone has much experience using motion effects on time-remapped clips. If I set 'position' or 'scale' keyframes in the Effect Controls, the changes are not always reflected in the program monitor, depending on the clip. If I try and set keyframes by dragging the video around the program monitor, it puts keyframes in places where I don't expect.
This doesn't affect all time-remapped clips, just some of them. Or maybe it does affect them all, just to varying degrees, depending on how extreme the time remapping is. I'm guessing now.
If I were to speculate further, I would say that the motion effect is operating on the clip before the time remapping gets applied. Again, just a guess, which is why I'm asking if someone more knowledgable has any insights before I pursue this much further..
Many thanks!

Hi Jeff, thanks for your response! Nested clips, you say? I have heard of these things but I can only imagine what they are and how to use them. Sounds like it's time for me to RTFM!
There's so much new stuff, it doesn't surprise me that I have to not only figure out the new feature, but the proper workflow to utilize it. I gotta ask: Do you know of any documents along the lines of "how to use modern premiere from the perspective of an antiquated premiere professional"? 4.2 was my bread and butter for many years and I knew it like the back of my hand. As such, it's kind of hard to stay awake sifting through Adobe's docs which generally assume no prior knowledge; although you giving me a place to start is a big help! But like I said: I gotta ask because it'd be great if there was something just for 'people like me.' (ain't it always the case? )
Again, thank you.

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