I think the university is largely correct here though they do undermine the air of transparency with meaningless (and potentially misleading) bits such as:
In two of the last six years (FY 2004 and FY 2010), the president, provost, vice presidents, and deans received no increase in their base salaries.
That is a bit like pointing out (correctly) that there have been literally thousands of days on which I worked at UM but did not receive a raise. Yes, sure, but irrelevant to any of several possible questions of interest.
My own experience with the university's salary and benefits system, both as a regular faculty member and as part of an internal salary study team, is that the university's administrative systems related to payroll are so arcane as to make Fizzbin look like checkers by comparison. It is not at all surprising that the Free Press messed things up, though perhaps they should have been more careful before publishing to make sure they understood what they were doing.
Of course, neither the original article nor the university response address deeper questions about whether the levels of administrative faculty employment and pay, or their arrangement across levels and task areas, are the correct ones.