Jonathan,
The code pen I have created works fine in IE9 on the VM. Changes here were unnecessary: the code pen does not replicate the issue, unfortunately.
Application of force3D doesn't seem to have an effect on the live file. I've spent some time reading a few articles here and blogs regarding performance using alternate threads or by using additional composite layers, but this doesn't seem to solve this particular problem. I fear it's something else interfering with the animation cycle, but I can't think of what it might be.
Using y or x instead of top or bottom creates a massive performance decrease in IE9 with the live file.
I've also moved all styles from inline to the CSS block in the live file to no avail.
The opacity property appears to be fully supported in IE9 and at least partially supported in IE8 -- although IE8 is not a concern for me at this point. Fortunately, opacity transitions work wonderfully in the IE9 instance and so do translations. They're all acceptably smooth. The animation issue seems to affect only the scaling and any animations happening during the scaling. The animation begins, may play for a frame or two, then skips to the end of the animation. It's quite jarring, as the rest of the animations look fine.
I wasn't able to find the Tools > Compatibility View Settings in IE9, however I opened the developer tools and made sure that IE9 is set to Browser Mode: IE9 and Document Mode: IE9 Standards.
Realistically I feel as though it's an inherited property from some other framework, since the animation works fine in the code pen in the virtual machine's IE9. The suggestions you're providing are the sort of thing I need, the sort of thing that might be the tweak that fixes the issue.
This isn't the only issue, but it's certainly the issue I'm focusing on for now. Hopefully these hints will get me that much closer. I'm going to start systematically removing frameworks that are non-essential until I figure out what is causing the issues. If I find something specific, I'll report back. If you think of anything that would be a good jumping point, let me know.