Double-check the auto-import folders in Options > Library.
For example, I map my D:\Media folder to M:\. I have to be really careful to _only_ use M:\ inside Media Center, because if I sometimes use D:\Media, there's no way for Media Center to know that the paths are actually the same so it can get a little messy.
If you need to switch paths, use the tool "Rename, Move, & Copy Files".