Sorry, no clue. The reason: not enough information.
AE has to work with so many different platforms, operating systems, third-party cards and varieties of media that diagnosing any one vaguely-worded problem can be a real pain.
With it, people will stand a fighting chance of being able to help you.
I'm using After Effects CS6 Ver. 22.214.171.124 on a Windows 7 64bit with 8GB of DDR2 RAM 800hz, a Phenom X4 9550 Quad Core, an NVIDIA 550ti 2GB RAM.
The original files I'm working with are canon dlsr .mov files. The files aren't corrupted when played in their original form, but anytime I export the video files, they corrupt. I'm also using the 3D tracker for some of the shots, and other shots are just the video with tracking. I export the files to h.264, avi, cineform, quicktime animation, quicktime h.264, uncompressed 8 bit and 10 bit, and all files no matter what get corrupted, sometimes in the same place other times they corrupt in random parts of the video. One really weird aspect was a video file from another project, unrelated to what I was working on was showing up in the corrupted parts of my video. I emptied all my caches, and cleaned what I could, and I still exported corrupted files. It doesn't matter what project, or what kind of video, but as long as I'm working with video clips, they export with corruption. I hope this helps a little.
Should I uninstall after effects, and reinstall it, or just update it?
Before you take the drastic step of uninstalling, running Adobe Cleaner and reinstalling (the best way to do it), try a test.
Transcode some of your dslr's H.264 clips to a lossless codec: I like quicktime Movies in the PNG codec for this. Import them, and use the Replace footage command to put the lossless clips into the appropriate AE comp.
And DON'T EXPORT FROM AE! Open the AE project in Adobe Media Encoder, and select the comp for your test. AME will let you render to all the media containers & codecs you mention.
No Joy? It could be a bad driver on a third-party card, you could have AE configured improperly.... we don't know. That's why it's good to answer that litany of questions linked to earlier.