There also seems to be an underlying problem with the sentence, whichever alternatives are chosen: what do the agreements in question say? They appear to be
agreements that [the corporations] are inclined to protect the universities’ interests
Butthis simply doesn’t make sense, either in colloquial or legal English! It’s like giving my landlord “an agreement that I want to pay my rent”. I might give him “an agreement that I will pay my rent”, or “an agreement to pay my rent”, but not that I want to pay it, since firstly I probably don’t want to, and secondly, the landlord doesn’t care whether I want to or not; he cares that it gets paid!
Perhaps there’s some other way of parsing the clause following “because” which I’m missing, which makes this make sense?
Regarding the question give, my first reaction is actually to agree with the OP’s preference:
The profits that the corporation earns from the exclusive-supplier agreements with the universities are surprising, because the terms of agreements that they are inclined to protect the universities’ interests are generally enforced.
I read this as follows: the agreements are to protect the universities’ interests (presumably: from the corporations), so provided they are enforced, one would expect them to limit or restrict the corporations’ profits. Thus, given that they are enforced, it is surprising that the profits are so large.
There is one piece of this reading that relies on idiomatic understanding of something not explicitly present in the words: the fact that surprising in a phrase like the profits are surprising typically means that they’re surprisingly large (or that it’s surprising there are profits at all), not eg surprisingly small. (Replace surprising with e.g. amazing, and this reading becomes pretty much unavoidable.)
The other popular option makes logical sense, as the other answer has argued, but seems less linguistically natural to me. I’m not sure why, but for some reason it seems unusual to have scrutinized unqualified in that particular position; I would expect well-scrutinized, carefully scrutinized, or similar.