First, make certain you've set the mime type properly for FLV:
This ought to be inside your httpd.conf
AddType video/x-flv flv
There is also to make certain the FLV isn't being gzipped, something similar to this:
<Location /> # Insert filter SetOutputFilter DEFLATE # Don't compress images SetEnvIfNoCase Request_URI \\.(?:gif|jpe?g|png|flv)$ no-gzip dont-vary </Location>
Hope that can help...