Not quite sure what the problem is here as I just redeemed two certs for domestic travel.
If you'd like to post the flights you're looking at I'll be glad to see if I can figure out what the issue is.
As for .bomb in general, at first I was not a fan of the site (I think they were the last major US carrier to allow seat assignments via the web)
but there are some interesting things the site will do (i.e. upgrades) and once you learn the quirks, it's really not that bad.
Anyways, feel free to put up some more info (or shoot me a PM) and I'll see if I can figure out why it's not working.