If you can't fix discrepancies in an acceptable amount of time then full transparency forces something unpleasant, and in this context it is potentially unhelpful to everyone.
A good example of transparency not helping is our sudden transparency about the activities of the NSA. Obviously that's not helping them. Though arguably it is helping us.
In a case where a company is intrinsically unfair to its employees and can't correct that, transparency would probably hurt the company but help all the employees - by sending a strong message that it's time to get the hell out of this crappy company.