Doesn't look like it does FLV though...
Reads the following input formats: MPEG-1, MPEG-2, MPEG-4, DIVX, XviD, non-encrypted VOB and VIDEO_TS, Quicktime .MOV, .DV, .WAV, Real Audio, Real Video, H.263, MP4 H.264, PGM, YUV, PPM, AC3, PCM8/16 bits, mulaw/Alaw, WMA-1/2, SUN AU format, MP2, MP3, AAC, 3GP, FPS1, ALAC, and even more formats
Converts the above formats to DivX, AVI XviD, H.264 MP4, MOV, DV, 3GP, Sony PSP, MP2, MP3, AAC, AC3, MPEG-1, MPEG-2, VCD, CVD, SVCD, KVCD, KSVCD, DVD, KDVD and MPEG-TS with complete control over encoding options.
It doesn't say it does on its features list, but check out the link below.
HOW TO ENCODE A MOVIE IN FLV FLASH VIDEO FORMAT FOR YOUR WEBSITE OR BLOG WITH FFMPEGX FOR MAC OSX
http://ffmpegx.com/flv.html