ProRes 422 file "corrupt" in Premiere (and Quicktime & VLC) but not in After Effects

We recorded a lengthy (c.90minute) seminar on an EX3 and an Atomos Samurai, to ProRes 422. We've noticed that the file glitches when it's played back in anything real-time, such as Premiere, VLC or Quicktime (we don't have a copy of FCP to test it on). What happens is that less than a second of picture will loop and stutter continuously for, say, 30 seconds, while the audio is just white noise. This happens seemingly at random (although at the same place in whichever software we're playing it back on), and infrequently: so far, in 90 minutes of footage we've found one 30" section which does this, and a few examples of it happening for a second or two.
BUT: as an experiment I tried importing the clip into AE, and it plays fine. I've been able to export a 1-minute long "patch" to a 4:2:2 MXF which doesn't glitch, which we've reimported into Premiere with no issues. Is there any reason why this should be - I had assumed that Premiere and AE would share the same low-level code used for playing back video, or is this not the case? Is it something to do with the fact that Premiere's trying to play it back in real-time while AE isn't?
Obviously, it's not a workable solution to have to keep running footage through AE. Is this a bug, or just one of those things?
Cheers
Nick

I had assumed that Premiere and AE would share the same low-level code used for playing back video, or is this not the case?
It is not the case.
Is it something to do with the fact that Premiere's trying to play it back in real-time while AE isn't?
That was my thought, too, given that even VLC stumbles on the clip.  AE basically 'renders' everything for playback.

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