Interesting! I tried deleting the folder where the Calibre library was stored, and then firing up the program again. The end result was the same, although it did seem to do something different in the output ("Upgrading database"). Here it goes.
Spoiler:
chapu@chapux:~/Downloads/calibre-0.6.28-i686$ sudo ./calibre
[sudo] password for chapu:
Traceback (most recent call last):
File "/home/kovid/build/calibre/src/calibre/gui2/library.py", line 608, in headerData
KeyError: 'ondevice'
link hasn't been detected!
link hasn't been detected!
Traceback (most recent call last):
File "/home/kovid/build/calibre/src/calibre/gui2/library.py", line 608, in headerData
KeyError: 'ondevice'
Traceback (most recent call last):
File "/home/kovid/build/calibre/src/calibre/gui2/library.py", line 608, in headerData
KeyError: 'ondevice'
Upgrading database to version 2...
Upgrading database to version 3...
Upgrading database to version 4...
Upgrading database to version 5...
Upgrading database to version 6...
Upgrading database to version 7...
Upgrading database to version 8...
Traceback (most recent call last):
File "/home/kovid/build/calibre/src/calibre/gui2/library.py", line 608, in headerData
KeyError: 'ondevice'
Traceback (most recent call last):
File "/home/kovid/build/calibre/src/calibre/gui2/library.py", line 608, in headerData
KeyError: 'ondevice'
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
Traceback (most recent call last):
File "/home/kovid/build/calibre/src/calibre/gui2/library.py", line 608, in headerData
KeyError: 'ondevice'
Traceback (most recent call last):
File "/home/kovid/build/calibre/src/calibre/gui2/library.py", line 608, in headerData
KeyError: 'ondevice'
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
QPaintEngine::setSystemRect: Should not be changed while engine is active
Is there anything else I should do to get rid of the old library, or is this problem something else altogether?