Ya it's really strange... could it be the history file? that's where the error was in the terminal.
Code:
IOError: [Errno 5] Input/output error: '/home/jesse/.config/calibre/history.plist'
it also gives me an input/output error when I try to change the properties on that file.
Edit: Does it pull from the same directory when using as root? because like it said it'll open as administrator