Thanks for helping out Trevor. When you say 'metrics table' do you mean the metrics section in the bar that appears after clicking "Show Advanced Settings" upon initial set up or the table titled "Top Metrics Against Segments" which appears after executing the segment comparison tool?
If it is the former, when I drag metrics over it excludes, not includes, them from the analysis. I would have to drag over 200 metrics that I am not interested to get the tool to run comparisons among the remaining 10-15 metrics I am interested in. I would have to do the same for the dimensions and segments loaded in my system.
I also tried dragging metrics of interest over into the "Top Metrics Against Segments" table after executing the segment comparison. The metric I drag over falls underneath a metric in the table 