The issue seems to be primarily one of case sensitivity. linux filesystems, and *some* OSX ones, are case sensitive, Windows is merely case-preserving.
My advice is, whenever switching to another OS, run Library Maintenance ==> Restore Database. Yes it will take a while, But it will make sure calibre can still see all your books.
You keep on switching between OSes and it's getting tiresome? Sorry, I've got no answer for you, other than... don't.
Choose one OS you will use, run the content server to access your books on another computer, and have done with it. IN a pinch, you can always transfer it over, as above.
One of these days, Kovid will eventually upgrade the content server to be able to fully manage calibre libraries (as in, write access). That should help things, but there is no ETA.
