Web support verified that the e-cert was not being priced correctly. At first I was told they showed that the e-cert was for 10% not $100 and I had to be a bit insistent that it was $100.

It cost me about an hour total time including 29 minutes and 18 seconds talking to web support. The web support person explained that the problem was even though the e-cert had a $75 minimum base fare restriction ual.com was enforcing a higher minimum therefore it picked an S for the return to increase the fare to be above the minimum. The total fare without the cert is $170.79 and with the $100 e-cert it was pricing as $129.80. I was told to purchase the ticket and a $100 credit will be issued within 3 days. This has rarely worked in the past so I am prepared to dispute it with my credit card if I don't get the credit on time.