Played GoT in 1.05 and all was fine. First time booting up in 1.06b (after DLing the update), and I've crashed twice. Each time after about 5 minutes. I've put all my advisers in one province (I'm playing as Gulltown in Crowned Stag). I know that was a problem in 0.1.1, so maybe it's still around? I'm having a lot of difficulty pinpointing what it would be otherwise. I've deleted the old GoT files from the /mod folder. Again, old version worked just fine, and I'm not running other mods, and I did not download SoI.
Wait, you downloaded v 0.2 and THEN updated to CK2 patch 1.06? Thats your problem there I think.