Clips exported with Media Encoder from AE are choppy (CS6)

Hi!
I'm using Media Encoder (6.0.3.1) to export clips from AE (11.0.4.2) so that I can work with them in PPro (6.0.5).
In Media Encoder I go to add AE composition and I've tried the YouTube HD 1080p 25 and the Broadcast HD 1080p 25 presets (the latter creates a much bigger file but I don't think the file size is the issue - for example, the biggest clip of approx. 1 mintute is 276MB).
The curious thing is that most of the clips that are exported are fine, i.e. they play back fine - the problem is that some of the clips go slow or choppy towards the end of the clip. So the last couple of seconds will be choppy. It basically looks like the frame rate isn't quite right.
Once exported from Media Encoder, I import them into PPro to do some more work - the problem with the clips is apparent when I play the original file in VLC (for example) or in PPro. So it seems like the problem occurs during the export from AE. When I export the video containing the AE clips from PPro the problem is obviously still there (wishful thinking on my part). I use AE just for keying and making some basic titles, nothing massively complex.
I had some problems with RAM preview in AE before, in other words, it wasn't playing the clips back in realtime and the exported clips with the problem look exactly like that (i.e. looks like the frame rate isn't right). I deactivated Enable Disk Cache in AE (Multiprocessing was already deactivated) and now I can play back clips ok in AE using RAM preview - even the ones that go choppy towards the end when they are exported with Media Encoder play back fine in AE.
Could Media Encoder be going back to some previous render files saved somewhere on my system and could that cause some of the exported clips to go choppy?
I'm new to Adobe so I'm just guessing here and I don't want to go about and delete stuff that might not have anything to do with this problem. As I've adopted the computer I'm working on from my predecessor and it's had several users since, the system is a bit of a mess and there are files all over the place. Empting the Disk Cache doesn't actually delete anything for example.
I'm really stuck here because I can't finish the projects I started working on with AE.... I would appreciate someone's input!
Many thanks in advance!
My system specs:
Intel Core i7-3930K, 3.20GHz, 16GB RAM, 64-bit operating system, GeForce GTX 680, Windows 7, Creative Suite CS6
Before using Media Encoder to export clips from AE I was just relying on Dynamic Link between AE and PPro by the way and that made all of the clips choppy for the whole duration (this was before I solved the RAM preview problem and I haven't checked if a working RAM preview would make a difference to dynamic link). So Media Encoder nearly solved the problem. I posted this original problem on creativecow (http://forums.creativecow.net/thread/2/1045810) but no one has gotten back to me about the new issue unfortunately.

Thanks for your reply!
I tried using Quicktime with PNG and it created a big file (1.18GB for a 1 minute long clip) that doesn't play back nicely in PPro unfortunately. But I then tried rendering the clip using a lossy format, H.264, in AE and it's playing back ok in PPro! I will just do that for the rest of the clips and hope that this is finally resolved. Many thanks for the tip!
Out of curisoty, do you know what might be causing the problem when I use Media Encoder?

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    Probably yes. Aside from the normal conversion with 2 pass VBR, which even under ideal conditions could require up to 3 times the duration of the footage (in your case this makes about 15 hours), you are causing additional operations to conform the frame rates on the Premiere level of things. Also, since this is handled as a Dynamic Link process, you may be a bit short on RAM, which may slow down things further. And then of course the usual with disk speed and file I/O etc.. So it more or less sounds normal, but you should not let the initial rough guesstimates discourage you. Many times these values will get much lower after a while of transcoding when the encoder has a much clearer picture and statistical data about how long it actualyl takes to encode so and so many frames...
    Mylenium

  • How do I export on Media Encoder CC and play on Premiere Pro CC without affecting the export?

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    You can just queue up the export right from PP, start the encode and then go back to PP to continue working.  No need to close anything.
    Doing this will slow down the export process, as PP will steal whatever resources it needs to run, often pausing AME to do so.

  • Can't Edit While Encoding With Media Encoder

    Does anyone else get this happening to them:
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    Encoding is a real CPU/disc hog ... heh, it's an intensive process. Trying to both encode and playback in real-time ... um ... if you've got a rig with say four CPU's with 128GB RAM, two really hot v-cards that the Adobe program actually love to play with, and all programs/cache/footage/outputs on RAIDed SSD internal drives, you can maybe do both at the same time.
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    Um ... VLC is playing the "straight" file, PrPro is playing back the file with all the other stuff added to it ... which isn't yet added to the file in reality, it's only instructions as to what to do to the file. So ... PrPro is essentially doing much the same work as when AME renders to an output simply to play the file in the program monitor.

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