Use of GConf can be an issue in some environments where the bus is not contactable due to permissions or network issues. Meld will detect this and fall back to using a flat-file configuration. However, this means that Meld may swap between the GConf and flat-file configuration, which isn't necessarily what you want.
You can force Meld to ignore GConf and store its preferences in an ordinary config file by invoking the following two commands at a shell prompt:
$ mkdir -p ~/.config/meld $ touch ~/.config/meld/use-rc-prefs
Start up Meld, and if you see the file ~/.config/meld/meldrc.ini, then you're all set. As long as the "use-rc-prefs" file remains in place, Meld will not use GConf for preferences.