Mine works fine, and i've a 2TB drive and i'm always adding games.
Personally I split XBLA, GODs & NXEs into their own folders within a Games directory. Then you can just tell FSD2 to scan for XBLA in the XBLA directory, and XBOX 360 games in the GODs and NXEs directories. I also find it easier to disable auto content scans, and just do a manual scan whenever you add games.
Try resetting FSD2's game data and starting from fresh, it can be a good idea to reset the game data when updating between FSD2 releases. You could always move the games FSD2 isn't showing to a seperate folder, and then getting FSD2 to scan that folder in addition to your games folder. Also ensure you are using the latest release of FSD2.
As for FTP, why use FTP when you can use Samba? I've had the odd issue with filezilla and found flashFXP to work better.
This post has been edited by tk_saturn: Mar 26 2011, 08:07 PM