This problem is caused by vShare not running any conversions on FLV files that are uploaded to vShare. When someone uploads a FLV file, the system automatically renames it and adds it to your site without any conversions whatsoever. Because of this, any badly encoded FLVs will not have any metadata that gets generated by the flvtool as it never runs. The whole seek/scan function of lighttpd (or any streaming system for that matter) relies on the metadata so without it, it doesn't work.

Since you have videos on another server, the best thing to do would be to install the flvtool on that server and run it on any video that does not automatically work. That's really the only thing that you can do with 2.6. In the next version, this should be easily fixable.