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The IME candidate window on Windows is offset some way below the caret position. This also affects standard GTK+ text widgets, not just the MD source editor.
This is a GTK+ bug, seee https://bugzilla.gnome.org/show_bug.cgi?id=663096
It should be pretty easy to fix, just replace the GetWindowRect call with DwmGetWindowAttribute if DwmIsCompositionEnabled is true. The only gotcha is that it'll have to be a soft dependency since it doesn't exist on WinXP.
I've attached a patch to that GTK+ bug, the fix hasn't been as straightforward, but has gotten rid of that calculation on screen coordinate space, and should work nicely from XP on.
We have prepared a new build of GTK+ that contains this fix. To test it, please download https://mjhutchinson.com/files/temp/gtk-2.24.20-2013-07-11.zip and copy the directories it contains "C:\Program Files (x86)\GtkSharp\2.12". You can verify it is installed by checking that "Help->About->Show Details" shows "GTK 2.24.20".
Seems to work correctly now.
The new GTK+ binaries have been included in the GTK# 2.12.22 installer, which is now in the beta update channel and will roll out to stable after we're reasonably confident there are no regressions.
Please reopen if this happens with GTK+ 2.24.20.