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\.