@
fvdham - if the check library didn't report any errors I'm not sure what good rebuilding it will do
Can you post screen shots of the settings you use in
Find Duplicates->Library Duplicates and
Preferences->Add Books
If you want to rebuild the database then I suggest you backup your library first, even though you think it is 'dodgy' its the best you have - right?
The
Library Maintenance->Restore database feature will rebuild the database from those metadata.opf files you have no doubt noticed in the book folders
Could take a while, you might want to let it run overnight.
BR