And can't say I've ever encountered this issue. Obviously it's not ideal, but I wouldn't worry too much seeing as everything else seems to be working.

When referring to your backup I meant at the time you created the backup; whether you ran the default backup or whether you tweaked the TKLBAM backup config (or used switches etc) to include additional files/directories/etc in your original backup. I was guessing that perhaps you have included something in your backup that ideally shouldn't be there and is overwriting something it shouldn't when you restore (and thus breaking confconsole).

One thing you could try is simply removing confconsole and reinstalling it, like this:

apt-get update
apt-get remove --purge confconsole
apt-get install confconsole