After Effects does not use the Mercury Playback Engine. That is a set of technologies that Premiere uses to playback a video stream.
The Mercury Transmit in AE is a technology for sending video to an external monitor, but I would not expect that to interfere with how AE renders anything.
You say you can scrub the timeline and it's smooth. What if you step through frame-by-frame? If that works, note that it will have cached the frames into RAM. Try invoking a RAM preview again and see if the problem persists.
What happens if you render your comp?
Ah...so not Mercury then. I emptied the cache and rebuilt the preview and I still had the same issue. Rendering the comp DID work, but is a bit of pain just for iterative work. I fixed it (oddly) by creating a new comp and rebuilding it from scratch and the problem seemed to disappear. It happened again though on a different comp, and once again rebuilding it solved the issue. I have no idea what's happening here...will just have to keep an eye on it and see if I spot any trends/consistencies...
Thanks a lot for your insight.
Elusive bugs are the worst! Keep an eye on it and keep us updated if you figure anything out.