Well I figured out how to switch the Windows and Alt keys
(go the Microsoft Keyboard icon in the System Preferences, then Options).
Funny thing is, I actually got this keyboard a while ago and switched the Ctrl and Alt keys from the start, I wanted to switch them back because I just got an HP laptop and I'm getting frustrated with the differing keyboard layouts. (So I know it can be done, and have done it myself, I just can't figure out how I did it [I thought I did it somewhere in the System Preferences but I've been through all the relevant ones and can't figure it out.]).