I'm running Calibre on a Mac, so it should detect case issues I think? The OS is case-sensitive after all.
Also, for the problematic books I can see the cover in COPS just fine...
Edit: I'm not so sure that OSX is case sensitive after all... it might depend on how the disk if formatted. I'm going to install Calibre on Debian in VMware and do a library check from there.
Edit2: I have my linux setup running in a VM, Calibre installed and pointing to my library which is still on my Mac partition. Still, no missing/extra
Maybe I'll copy my library to the linux partition and try again.
I found out that when I modify the author from "author" to "author_x", the filename is correctly written, thus the book can be downloaded in COPS too. If only I could find a way to mass change the authors and then change it back to the original names again...