problems with video length export

A likely cause is one of your source footage items.  The easiest way to resolve it is probably to use the After Effects Render Queue to export an interim file (Best Settings - Lossless is usually a good choice).  That movie will be really large.  Check it and assuming the frames advance as expected add that to Media Encoder to create your delivery file format.  

Without exact info on your system, your render settings, the project's contents and so on we can't realyl tell you much. This could be anything from corrupted caches to framerates getting messed up with "bad" settings to, of course, failing hardware acceleration. In the latter case the least you could do is to turn off GPU-accelerated encoding in AME and see how it goes... For anything beyond that mauch more specific info is required.

Mylenium