I can reproduce it: I have the same problem using the GUI.
The problem seems to show up just with some files.
I'm on Natty too (but it's a fresh install)
** Changed in: meld (Ubuntu)
Status: New => Confirmed
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https://bugs.launchpad.net/bugs/781524
Title:
Warning: g_object_set_qdata: assertion `G_IS_OBJECT (object)' failed
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