I have a problem with specific FLVs too.
For the past year I've been grabbing videos from the Vimeo site.
Discovered Video Thumbnails Maker & thumbnailed around 700 vids. The few FLVs that failed worked when I went Gold and used the Extreme engine.
But recently I think Vimeo upped to a newer version of Flash. They ALL fail for me now. But those very same FLV files are successfully played & thumbnailed by KMPlayer & Media Player Classic.
I'm up to date with latest codecs - K-Lite Mega Codec Pack. And YouTube FLVs are ok with Video Thumbnails Maker.
Here's a typical Vimeo FLV file that fails for me. It will need to be retrieved from the Browser cache.
http://www.vimeo.com/4527934 (3.3MB in size)
Obviously I could use the two players mentioned above to make thumbs, but Video Thumbnails Maker is a whole lot better, and increasingly so!