Well, firstly, what version of VLC are you using ?
Secondly, approximately how old are the .FLV (Flash Video) files ?
Sites such as YouTube, have traditionally used the .FLV files, but the newer standards such as .MP4, and .Webm are of course replacing
the old .FLV video files.
I would suggest the free app called 'MediaInfo' - this will tell you a lot of technical details about your media files,
weather they be audio, video, etc.
I personally have a lot of the old .FLV video files from the 'old' days of YouTube.
A lot of the very old/early .FLV Video Files on YouTube were poorly encoded and often had incorrect/non-standard frame rates,
and other issues.
Because YouTube now has a video quality option - it is possible to re-download a lot of the old videos again, with a higher
quality than before, and also you sometimes/often get the option of downloading the video as an .MP4
I mention that just in the event that even if the latest version of VLC still has problems playing some of your .FLV video files,
there is possibly another option for you.
The only other option i can think of is to re0encode (Re-Save) your current .FLV Video Files from either a video converter
or a free video editor, such as AVIDemux.
I do hope I have been of some help