You are absolutely correct. When Durkon happens to prepare the right tools, he uses them effectively. Unfortunately, this happens so rarely that, when Durkula prepared correctly for a job, Belkar even said "He had a spell prepared that can actually solve our problem! That proves he can't possibly be Durkon!"
Which is why he is the best "prepared caster" and not the "best prepared" caster. When you're the "best prepared" caster, your teammates don't usually comment on how you're never prepared.