I had similar problems two weeks ago but failed to reproduce them after 
updating to latest master.

It looks similar to known bug: https://bugzilla.gnome.org/show_bug.cgi?id=768300

That slowdown was fixed in current master and meld-3-16 branches near 
2016-07-02 by 
https://git.gnome.org/browse/meld/commit/?id=080a20c18c4e7970b690c4785663fe26333fc313
and 
https://git.gnome.org/browse/meld/commit/?id=8f2dcd1baceb8f297f67f550c6c707e72d3749d1

But there isn't yet any meld releases incorporating those fixes.
So you may try the fixed version by running bin/meld from a fresh checkout of 
meld-3-16 branch of https://git.gnome.org/browse/meld
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