This happens to me, too.  Do randomly dies -- I only notice when I go to use it, and it's no longer running.  I am running openSuse 11.1, and when I run Do from the command line, this is the output:

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davidz@kauai: ~> gnome-do

** (Do:6570): CRITICAL **: gnome_desktop_item_get_localestring: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_localestring: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_string: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_string: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_localestring: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_localestring: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_string: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_string: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_localestring: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_localestring: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_string: assertion `item != NULL' failed

** (Do:6570): CRITICAL **: gnome_desktop_item_get_string: assertion `item != NULL' failed
Could not read Gnome Bookmarks file /home/davidz/.gtk-bookmarks: Could not find file "/home/davidz/.gtk-bookmarks".

** (Do:6570): WARNING **: The following assembly referenced from /home/davidz/.local/share/gnome-do/plugins-0.6.0/addins/Do.GNOMETerminal.1.0/GNOME-Terminal.dll could not be loaded:
     Assembly:   gconf-sharp    (assemblyref_index=1)
     Version:    2.20.0.0
     Public Key: 35e10195dab3c99f
The assembly was not found in the Global Assembly Cache, a path listed in the MONO_PATH environment variable, or in the location of the executing assembly (/home/davidz/.local/share/gnome-do/plugins-0.6.0/addins/Do.GNOMETerminal.1.0).


** (Do:6570): WARNING **: Could not load file or assembly 'gconf-sharp, Version=2.20.0.0, Culture=neutral, PublicKeyToken=35e10195dab3c99f' or one of its dependencies.

** (Do:6570): WARNING **: Could not load file or assembly 'gconf-sharp, Version=2.20.0.0, Culture=neutral, PublicKeyToken=35e10195dab3c99f' or one of its dependencies.
[Error 22:25:18.517] "Gnome Terminal Profiles" 
    (GNOME.Terminal.ProfileItemSource) encountered an error in UpdateItems: 
    Could not load file or assembly 'gconf-sharp, Version=2.20.0.0, 
    Culture=neutral, PublicKeyToken=35e10195dab3c99f' or one of its 
    dependencies. 
Universe contains 246 items.

None

Could not read Gnome Bookmarks file /home/davidz/.gtk-bookmarks: Could not find file "/home/davidz/.gtk-bookmarks".

** (Do:6570): WARNING **: Could not load file or assembly 'gconf-sharp, Version=2.20.0.0, Culture=neutral, PublicKeyToken=35e10195dab3c99f' or one of its dependencies.
[Error 22:30:16.307] "Gnome Terminal Profiles" 
    (GNOME.Terminal.ProfileItemSource) encountered an error in UpdateItems: 
    Could not load file or assembly 'gconf-sharp, Version=2.20.0.0, 
    Culture=neutral, PublicKeyToken=35e10195dab3c99f' or one of its 
    dependencies. 

Unhandled Exception: System.TypeLoadException: A type load exception has occurred.
at NDesk.DBus.PendingCall.set_Reply (NDesk.DBus.Message) <0x00032>
at NDesk.DBus.Connection.HandleMessage (NDesk.DBus.Message) <0x000d1>
at NDesk.DBus.Connection.Iterate () <0x00023>
at <Init>c__AnonStorey0.<>m__0 (intptr,NDesk.GLib.IOCondition,intptr) <0x0002a>
at (wrapper native-to-managed) <Init>c__AnonStorey0.<>m__0 (intptr,NDesk.GLib.IOCondition,intptr) <0x00049>
at (wrapper managed-to-native) Gtk.Application.gtk_main () <0x00004>
at Gtk.Application.Run () <0x00007>
at Do.Do.Main (string[]) <0x0028a>

davidz@kauai:~> 
None

davidz@kauai:~> 

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Please advise,
David