Until very recently I didn't have this problem because I was using Puppy Linux which runs simply as root and that's it, but now that I switched to LinuxMint it's a whole new ball game with all this confusing nonsense of permissions, priviledges, accounts etc

but that's a discussion for another time and since most of the people would be using mainstream distros, testing calibre-portable on LinuxMint is the right way to go about it.
I don't know enough about linux to make sensible suggestions..
As for USB/portable media adn FAT32, isn't it limited in size? I am using at the moment 60Gb portable HDD for the testing.
When I tried it with windows (two desktops and laptop, all running XP) I didn't have any issues (it was formatted NTFS)?