It's possible that the deed and the restrictions were filed and recorded separately and the deed just makes reference to any encumbrances if any.
But I have to agree with you JK, that the title search should have found any recorded documents that attached to the property. For a title company saying that it is not their job to find such documents is just absurd.
OP, have you talked to your lender about the problem? You did pay for a lender title police right?