What causes replays to come out very dark?

Per Steam support, this (the codec part) solved it:

Thank you for contacting Steam Support.

You may wish to select a different rendering output codec.

Note that video compression techniques often rely on reducing the range of colors and brightness used in a frame.

Using a different codec may create better results.

You may also try increasing the Brightness Levels in the in-game Video options menu prior to rendering the replay.

For more information and options, please refer to the TF2 Wiki replay article linked below.

http://wiki.teamfortress.com/wiki/Replay

If you have any further questions, please let us know - we will be happy to assist you.

The same forum post you linked to has a possible solution by using windowed mode.

Other than that, it could be a driver issue - try installing the latest & greatest ATI drivers.

Also, if you are running dual video cards try disabling one of them. Dual GPU setups can exhibit weird behaviors.