I have this problem for some time too, starting after some upgrade session of 
gutsy.
But I can not say which update, because I did no diffs for a while.

Today I noticed, that I can see file diffs when being user xyz but can't
when being root.

So I compared gconf settings of apps/meld and made them look equal for user 
root.
User xyz had some settings unset which root had set.

After this change I can use file diffs as usual (hopefully).

So I assume that some setting changed it's behaviour and fails with a
new meld...?

-- 
Meld fails to display file diff interface
https://bugs.launchpad.net/bugs/129352
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