Hey Uriel,
Yes as you’ve already discovered there are a few one one trick pony applications out there that handle this with mixed results.
I use the free plug-in Perian to get QuickTime to playback .FLVs files natively. Then it’s just a matter of exporting it straight out of QuickTime to ProRes 422 (HQ) or whatever codec you want to work with.
Give it a go and let us know how you make out.
Joe Truesdell
Technical Director
globalmechanic.com