UPDATE: I took a look at your problem and I think I know what the issue is. When Windows works with folder names, it intentionally cripples itself and limits paths to a max length of 255 characters when specifying relative paths. So if you specify a path to scan like this:
jav-it catalog -d my_videos
Where "my_videos" is a folder under the "jav-it" location, it will be considered a relative path and will be limited to a max path length of 255 characters. However if you specify your command like this:
jav-it catalog -d c:\temp\jav-it\my_videos
Then Windows won't operate under those restrictions and performs as expected. This unknown/obscure behaviour is pretty lame, but I assume Microsoft did it for some backwards compatability reason. So as a temporary workaround, try specifying absolute paths in your command and let me know if that solves your problem. In the next version of Jav-It, I will internally convert all paths to be absolute so that regardless of how users specify it, Windows won't bug you again.
Since I don't know the original command you were using, I'm only taking a guess that this is your issue. But hopefully you can try it out and confirm for me if this helps or not! (^_^);