Had to have been

Is this sentence correct:
"There had to have been a reason why she didn't want to talk to me, and I prayed it was because she was trying to protect Sachs."
I think it has to be either "There had to be a reason ..." or "...why she hadn't wanted to talk to me".

"There had to have been a reason" is fine. It is similar in meaning to there must have been a reason. The speaker or writer is speculating on something that has already happened. (The verb tense is, I think, past perfect progressive.)

Perhaps somebody else will offer an additional comment or two. In any case, that usage is perfectly fine.

The use of 'have been' implies that the reason may have lapsed since then. ;-)