If she just wants to READ your books, run the content server on Ubuntu and give her a browser shortcut in Firefox (a little bias here
).
She can download selected titles from your system.
BTW are you running Calibre 1.x (not the outdated Ubuntu Repository version)?
I thought there was a Library pathname cleanup (shorten) tool to avoid this issue.
Also:
If you do copy, keep the Library name very short and at Root level:
eg. c:\Lib1
Copy the CONTENTS of your folder into that folder.