I think that English is more flexible in the number of verb tenses you can use in the subordinate clause of a subjunctive type sentence.
(That's what makes matching DL's translations so hard, English speakers have so many different ways to flip the words and STILL be grammatically correct!)
Actually, I believe it is in the imperfect subjunctive too: http://www.verbix.com/webverbix/English/understand.html
You should always use the subjunctive after «pensar» because, just because you think something, does not mean it is true. Since it is uncertain whether it is true, the subjunctive is the correct mood. You would use "tinha" in situations where things are certain: "Eu vi que ele tinha um mapa nas mãos." I definitely saw that he had it, so we use the indicative mood "tinha."