While trying to install Starcraft I tried switching back to using Explorer as the shell (didn't work anyway), and then switched back to LS. When I rebooted and fired up Foobar, all my settings were lost. Why would this happen?
Did you by chance try Foobar when you had switched to Explorer? Just curious if that's when the problem might have happened.
It started, since it's in my startup folder, but I didn't change anything. Was that enough?
I've done that many times (FB2K and FF are pretty much always running), and never had a problem. Whatever it is, I don't think it's directly LS, or even shell, related. I wouldn't be surprised if it's related to whatever caused SC not to work, though.
One thing, how did you install FB2K? Did you check the files? IE, it could have swapped from Program Files\Foobar2000\ to user\Application Data\Foobar2000\.