This affects me too.
Some googling brought me to this old article and Launchpad bug:
http://ubuntuguide.net/fix-altprint-screen-current-window-screenshot-not-working-in-ubuntu-10-10
https://bugs.launchpad.net/ubuntu/+source/metacity/+bug/642792
Disabling the "Magic SysRq Key" as suggested in the linked article seems to
have fixed the issue for me:
$ sudo sysctl -w kernel.sysrq=0
However Shift+Print Screen to take a screenshot of selected area still
doesn't work at all for me but that may be another bug.
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https://bugs.launchpad.net/bugs/1072199
Title:
Alt+Print Screen only takes picture of the HUD
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