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What codec are you using? What kind of hard drive is the file playing from? A lossless HD file can typically only be played back with fast video RAID drives. Odds are your hard drive simply can't read the data fast enough to playback.
Try rendering preview versions of the files in H.264 codec (or similar) for viewing at full speed.
Right after I posted my question I realized what was wrong. I was trying to import the .mpeg file directly into After Effects instead of exporting as a .avi file (from Adobe Premiere) first. I remember reading somewhere that After Effects doesn't work real with with .mpeg, you need to convert to .avi or .mov first and THEN import into After Effects. The only problem is that when I export the .mpeg into a .avi file it looks like crap....
I stepped on your reply as I was writing an update. You asked about what codec I'm using. Well, I'm totally confused right now. When I select "Export-->Adobe Media Encoder", I have "MainConcept Mpeg" (outputing to MPEG2). I can't remember how to see the available codec's, something I just found 5 minutes ago but don't remember how I did. Whatever screen it was that showed all the available codecs I remember seeing Xvid (for mpeg4).
I have to start writing down what I do to get the results I want when by some miracle I do get good results. I don't work with video editing enough to know what the heck I'm doing.
(FYI, the drive I'm using is an internal SAS 7200 rpm drive).
Alison, HD footage+huge file = high data rate per second. That's all that counts. It's quite possible to play back large files, but this requires a different means of lowering data rates which in turn means you need to use some sort of compression. For just checking on your computer, WMV would be preferrable, but you should be able to use H.264 as well, even more so if you use alternate players like VLC which handle this mucho better than Windows Media Player. Likewise, you can of course use Quicktime H.264/ MP4. As for your other problem - AE does handle a variety of of MPEG flavors as source files, which should include all standardized formats produced by (professional) video cameras, meaning MXF, HDV and several MPEG-2 vraiants. AVCHD is supported in CS4 only, though. Other formats e.g. such as used in digital photo cameras with movie recording functions may not be covered, it just depends. There's simply too many variations out there to cater for them all. So if you have the time, it may still be worth giving it a try to avoid those pesky conversions in the future.