Hi,
I have tried this with several .mov files of different sizes, both in pixels and in duration. (from 6 minutes to 5 seconds)
When I encode to F4V everything is fine.
When I encode to FLV with ON2 and 1 pass everything is fine.
When I encode to FLV with ON2 and switch on 2 pass the progress bar stops at the half way point for a while (presumably at the beginning of the second pass) and then Media Encoder closes. A zero byte file is left in the directory.

I am using CS4, on windows XP. I have downloaded all updates for my Adobe products. I have restarted my computer. None of these things make any difference.
It crashes every time with 2 pass on.

Addition to post.
I have now reinstalled flash pro CS4 and media encoder. BEFORE checking for and installing any updates I tried encoding a completely new file and experienced exactly the same crash when set to ON2 2 Pass.

I then installed all updates again. No change, same crash of Media Encoder.

Mark