Are you using an FLV located within Moodle or trying to link to an external FLV file ? An FLV hosted within Moodle shouldn't have http:// at the start of the URL, the path stored is relative to the config file. If the file is external and you can post the URL here, i'll give it a test and see if I can work out what is happening.
Depending on the URL, the flowplayer flash video player doesn't accept the URL 'as a whole' it has to be split up, though this happens on-the-fly at the point the plugin tag is generated and shouldn't change what's in the config file.
There is some code which will re-write a flash URL and remove the .flv when the video source is first added if you have a flash server integrated with AutoView. However, we haven't released anything that works with this yet (though we have it working internally), so unless you've tried to configure a third party flash system (i'm not aware of one) to work with AutoView in the Module setup pages this code shouldn't be active. Even if the code is active, you should be getting a popup choice box when you first add a video source asking if you want to use the flash server to improve video performance.
If you want to re-write the underlying config file, make sure the editing mode is switched off, otherwise the changes will be overwritten. If editing mode is off, then the changes can't be overwritten.