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I'm having exactly the same issue, Ubuntu 11.10, gnome-shell. Calibre 8.59 and 8.60. debug output is
calibre Debug log
calibre 0.8.60
Linux-3.0.0-22-generic-x86_64-with-debian-wheezy-sid
Linux
('Linux', '3.0.0-22-generic', '#36-Ubuntu SMP Tue Jun 12 17:37:42 UTC 2012')
Python 2.7.3
Linux: ('debian', 'wheezy/sid', '')
Starting up...
Started up in 12.87 seconds with 2281 books
(process:2188): GLib-CRITICAL **: g_main_context_pop_thread_default: assertion `g_queue_peek_head (stack) == context' failed
BUT, if I double-click the .mobi file I want to add whilst calibre is open, it is added successfully.
Hope that helps.
Vincent
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