The report from the group that did salary reviews is actually surprisingly good.

Basically, they did a regression analysis based on a whole bunch of factors (years worked, faculty, department, merit score from performance reviews, performance awards, etc. etc.) to predict what a person's salary would reasonably be expected to be based on all of those things. They did a non-gendered analysis first and identified a number of outlier anomalies (people who were being paid significantly more or less than could be explained by their position and performance), then adjusted those to where they would be after an appropriate adjustment and re-ran the analysis with gender included.

The "anomaly" was simply that women were systemically being paid less to the tune of a few thousand bucks, even after controlling for other factors. There wasn't a formal system in place that was distinguishing between male and female employees when assigning salary, this was just the cumulative result of hiring salary and salary adjustments over the years, which for whatever reason, favoured men to the tune of a few thousand dollars. If you eyeball the data to pick out an average salary, this represents a pay gap of about 2%, which would be easy enough to miss as a systemic problem if you didn't actually sit down and do the analysis.