Converting results in somehow b0rked files, but if all you want to do is to play them using e.g. MPC try the following:
ffmpeg -v quiet -i "Counter Monkey - Pathfinder Live! (Session 1, Part 1).flv" -vcodec copy -acodec libvorbis output_part1.mkv
/edit:
seemingly non-b0rked files:
1. extract using FLV Extract
2. ffmpeg -v quiet -i "Counter Monkey - Pathfinder Live! (Session 1, Part 1).flv" -vn part1.aac
3. muxer -i "Counter Monkey - Pathfinder Live! (Session 1, Part 1).h264"?fps=25 -i part1.aac?language=eng -o part1.mp4
"muxer.exe" is from
L-Smash standalone.