You can tell immediately that it's a problem file because the video length in the time display is given as "--/--". (It seems strange that it doesn't know the length though, because the time slider knows where it is. (Or is it smart and using the file size instead?))
Also, in the messages window, it prints out: "avformat debug: Trying to seek too far : EOF?", loads of times starting immediately after: "avformat debug: detected format: flv".
I can't see anything that the problem files have in common apart from having "FLV1" as the codec. But I've also tested many FLV1 files that play and seek absolutely fine. I couldn't localise the problem further, except that all the files work perfectly fine in 0.9.9. I've had to keep it installed for this.
![Neutral :-|](./images/smilies/icon_neutral.gif)
If this helps, I uploaded a sample which causes the problem to streams.videolan.org. Filename is "#166 Faith in a Boy (2).flv".