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[mrk <cvs-src@xxxxxxxxx>]

I've just checked this case with strace and it doesn't looks to me that
it ever trying to create gtg.desktop in /home/mrk/.config/autostart/
when i check the option. But when i uncheck it checks if this file is
available in right place:

stat("/home/mrk/.config/autostart/gtg.desktop", 0xbfbfc5a8) = -1 ENOENT
(No such file or directory)

When i check this option it's try to stat in /usr/local/lib/python2.6
/site-packages/:

stat("/usr/local/lib/python2.6/site-packages/gtg.desktop", 0xbfbfc5a8) =
-1 ENOENT (No such file or directory)

May be it take you some hint about the problem.

-- 
State of the 'Start GTG on every login' checkbox doesn't survive gtg restart
https://bugs.launchpad.net/bugs/533318
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Status in Getting Things GNOME!: Confirmed

Bug description:
State of the 'Start GTG on every login' checkbox doesn't survive gtg restart. 
Indeed it resets after every calling of the Preference pane.

This is may be somehow related with bug #533157.

It would be great to see this included into 0.2.4.