I'm pretty sure Do does not pop up a dialog to say invalid drag type.
This must be popping up by Nautilus.  If that is the case, then it makes
sense that docky hides as the popup belongs to Nautilus, which overlaps
the dock.  Ordinarily the dock can just ignore this desktop window, but
with a popup I think it now becomes a 'group' of windows and 1 in that
group overlaps == autohides.

Also would explain why you get the error just dragging to the desktop.

Try to narrow this down more.  Don't run Docky for awhile, see if it
happens.  If it does ==> not GNOME Do's fault, file with Nautilus.  If
it doesn't happen, run Docky but disable autohide.  Does it still happen
then?

-- 
Gnome hang
https://bugs.launchpad.net/bugs/433817
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