Sorry to open a dead thread, but I'd like to add some more information about this issue because I don't think it's a data rate issue. I just had a similar problem. I've been working on an animation project in AE at 1920x1080 23.98 and I thought I might save some time by rendering half-resolution clips to work with in FCP, knowing I'd probably be re-rendering a few times while I edited. So I output a 960x540 ProRes HQ clip, which did take very little time to render. I then created a 960x540 ProRes HQ FCP timeline to edit in. I immediately saw the gamma shift that sgmitch described. I'd never seen anything like it before, and I've done 1080p ProRes HQ editing on this system with no trouble in the past. So I did a little Googling and came across this thread.
I thought I'd test out the disk speed question by rendering a bit of the same sequence at 1920x1080. The data rate on that clip is 19.2 MB/s and the data rate on the half-resolution 960x540 clip is 8.6 MB/s. The full-res clip plays with no gamma shift in a 1920x1080 ProRes HQ timeline. But it turns out the half-res clip also plays with no gamma shift in that same 1920x1080 timeline, with or without rendering. When it's not rendered in that full-res timeline, it has an orange bar over it, but plays back fine. The half-res clip also has the gamma shift when playing in the Viewer, but not in QT Player. The 1920x1080 clip displays the gamma shift when placed into the 960x540 timeline and rendered. It will not play without rendering. 960x540 clips rendered using the Animation codec (33.3 MB/s) don't have a gamma shift in the Viewer or when played in a 960x540 Animation timeline.
There are no RT options in the drop-down menu for 960x540 timelines in any codec I've tried. I suspect the problem is caused by using non-standard resolutions with ProRes HQ, and it might also have something to do with the way AE saves gamma information in ProRes files. I know that came up when Frank Capria did that test last year comparing DNxHD and ProRes.
The obvious solution is to edit with standard frame sizes when using ProRes HQ. I know that's what I'll be doing.