Exported file differs from that created in workspace

Hi,
I have created a 5 minute movie which is bookended by two different After Effects animations.
When I preview the movie in CS4, and even in Media Encoder, it plays perfectly. However, the exported file (I have tried WMV and AVI) puts the introductory After Effects animation at the end of the movie as well, in place of the one which it is supposed to end with!
I basically have my introcuctory animation both at the beginning and at the end, despite the fact that it doesn't appear this way in After Effects, Premiere CS4 or Media Encoder.
Any clues?!
Many thanks

Are the AE Comps Dynamically Linked, or did your Export from AE, then Import them into PrPro?
Good luck,
Hunt

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