Hi,
seems that something works wrong in your case or maybe your file/s are a little broken and VLC dosent read FLV Header correctly so that you get this playing problems.So I cant imagine that all of your flv files are broken.So you can try to use ffmpeg tool to let create new header in your video without to convert the video.You just need to use copy commands like this....
Code:
ffmpeg -i videoX -vcodec copy -acodec copy videoY
...just enter the video name (123.flv) for videoX and for videoY write the output name (123_fix.flv).You can enter this command in CMD window but dont forget using also paths or just copy the CMD.exe also into your ffmpeg folder + the video xy you wanna fix etc.Mostly I do this if you have done some records and files are not seekable.Just try this.
Normaly VLC does play flv files ok.Some older versions of VLC could handle flv files better (faster playing and also mostly seekable for broken files) but older versions could not play speex audio codec.Anyway,so if you only get the problem with VLC to play your files then try maybe to uninstall your VLC + settings and reinstall it fresh or check your video file in VirtualDub (use flv / ffmpeg / Quicktime plugins so these you need to download extra).Or if nothing helps then upload any problem video file of your (1 minute or so) where you got the problem to check this out.
greetz