I've run into the same issue. The trouble is iTunes will look at your advanced settings for the location of your library and if the drive/location does not exist it defaults back to the c:\ folder.

Your PC must be configured that each new device starts at the next available drive letter after c: and continues from there, so it really matters the order the drives are connected.

What you could do for now is go into the advanced settign and repoint iTunes to the current drive letter with your music (I do this all the time). Unfortunatley it will porbably re-read the library as iTunes thinks this is a new one, but all your playlists, etc should still be there.

I cannot think of it off hand but will see fi I can remember, there is a way to force a specific device to a drive letter, so each time you connect the SD card it gets D:, the external hard drive E: and your other CD drive F: (or something like that).