Can't export Quicktime H.264 from AE CS4

Whenever I try to set the export module to Quicktime H.264 I immediately get the error/message, "For reliable output with H.264 compression, please choose it directly from the Output Module Format menu instead of via Quicktime."
If you try ro render, you only get an error and there is no render.
What could be going wrong? Is a plugin not working? The only thing I can think of is I updated to Quicktime 7.6 a few days ago. Anyone else experienced this problem?

I'm encoding at 640x360. I usually use profile level 4.1, but this is only going to be directed towards software not hardware. There are work arounds to this, lots of them. Like encoding using Quicktime Animation codec and then re-encoding to Quicktime H.264 out of PP CS4, Sorenson Squeeze, or even Quicktime itself. All will work well. But the thing is that a person shouldn't have to go through a two-step work around like this. You want to maintain quality but Animation files are relatively huge. (By the way, its funny how PP CS4 has no problem exporting QT H.264).
How would I use Adobe Media encoder directly? Just drop the project from AE into the queue?

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