My flv workflow is to Export a self-contained QuickTime Using Current Settings and then use Soronson Squeeze with the On2VP6 codec. It's worked well for me without dramatic gamma shifts. The have a trial version.
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One thing you could do is apply a gamma shift effect to compensate for the output.
You could export your timeline as a clip or as XML and bring it into Premiere Pro. Then apply a Gamma Correction clip. I'm hearing that a 1.2 of the original will probably work well. So, a value of 12 from the default value of 10 would be a good place to start.
Then export the media via AME and render to Flash.