The e-certs are definitely problematic, but one trick I have learned that may make the system work is to click on the "full flight search" option from the homepage rather than trying to enter it directly in the flight search right on the homepage.

I've got no idea why that would make any difference, but a number of times I have been able to get the website to accept the e-cert (and actually apply to discount properly, believe it or not!) when I click through to the full flight search.

Hope that helps.