There is a huge open source Flash community over at
Recent News Open Source Flash, good place to start for IDE's, video stuff, class libraries, animation engines, database tools and debugging loveliness. Have a look there for FLV tools.
Also, I've used this in the past (I use Flash Pro now so haven't used this for a few years) but it created FLV from MPEG and AVI when I needed it to:
Riva FLV Encoder - Free software downloads and reviews - CNET Download.com