So I have my Wii games in a WBFS folder on my external HDD which means they are in there in folders and I was able to just point Dolphin at the WBFS on a older revision and it picked the games up but my current folder of dolphin does not pick the games up inside the folders in the WBFS folder. Was that done on purpose or did someone change something that caused this issue?
Are you running Dolphin as an administrator to avoid issues with saving things to it's folder under Program Files under Windows 7/8?
My guess is that this is due to an issue where network shares are not shared between users on a PC, so the admin user doesn't see the shares setup by a non-admin one. The easiest solution is generally to move Dolphin to a location outside of Program Files that Windows UAC won't apply to. You can then run Dolphin outside of admin mode; it will be able to save things to it's folder normally, and should see the network shares.
Since I am running a portable SVN I dont have it installed at all. The WBFS folder is on an external HDD that is physically attached to the computer and I have it set in Dolphin as such.
do you have search subfolders checked in the config dialog?
Thanks that is what I was missing. Games now appear in dolphin.