There was a bug in QuickTime that set a meta tag in your QuickTime movie showing the last playback size when you closed the file. This shows up in finder and is read by After Effects.
Try opening the file in the QT player, making the footage full size, then closing, then open in After Effects.
If you have QuickTime pro installed then make sure that you're opening in the regular QuickTime player. You should be on 10.9.2 I am assuming that your AE version is CS5.5
Have you seen this thread:
CS5.5 is not supported in Mavericks. I'm surprised that it even works at all.
Thank you Rick! That makes sense, the only problem is that Quicktime 10 doesn't allow me to view "Actual Size", that option is grayed out in the menu. It seems to be clamped to whatever the resolution of my monitor is. I do have an Apple Display that's a bit larger than the one I'm currently using but it's still not 4K, so I presume that the resolution will still be limited.
I tried viewing Actual Size in Quicktime 7 Pro, saved the file, and that updated whatever metadata Finder uses, because that shows the correct info now. After Effects still imports it as 1364x767 though, .
I created a dual boot system to maintain 10.6.8 on my computer. Some of my projects require applications that run in 10.9 so I use Mavericks quite a bit. Restarting the computer to boot into Snow Leopard for CS programs was somewhat annoying, so I began running CS in Mavericks and was pleasantly surprised to find that it works fine. I'm currently back in Snow Leopard, but the problem persists both with Quicktime 10 graying out the "View Actual Size" option and AE importing at the wrong resolution.
UPDATE SOLVED: Using QT 7, setting actual size, saving, then importing to AE CS5.5 worked in Snow Leopard. I did the process over and it worked.