I have a USB hard drive with a FAT32 and NTFS partition with the Fat32 partition being the first partition on the disk. FSD sees the partition in the file manager and I can select the xex and launch games just fine but the games don't show up in the Xbox 360 games category of the dashboard. The games are located in USB:\games\ and xexmenu sees them when I use that but for some reason FSD doesn't. In my content settings I've configured all the file paths properly and I've tried deleting the database but nothing has worked. Any idea what the problem is?

If I add each folder individually it works so I guess I'll do that.

Try increasing the scan depth, if path is set to \games then e.g. .\games\disk1\<a game>\default.xex would need a scan depth of 2 deep.