Trying to figure out why, by default, the Fedex rates that are returned are not the discounted rates that we're expecting. Found a good post on the Magento forums relevant to this:
http://www.magentocommerce.com/boards/forum/viewthread/303546/#t473550
They referenced a Magento bug report that I couldn't find:
Issue #14644
I'm currently on Enterprise 1.12.0.2 (I know I know, behind 2 major point versions. If it turns out this issue is due to be being behind, that will be a first).
Perhaps it's just that by default they expect merchants to charge their customers list price and keep the savings for themselves. That wouldn't be completely unreasonable. But it's surprising that there isn't at least a configuration option for this.
UPDATE: I noticed that I got a downvote and close vote. While this question may in part relate to a business decision that's outside the scope of a proper SO question, I think that this is still a useful question to have a cannonical answer.
After a decent bit of searching, I wasn't able to figure out why my rates were incorrect and Fedex developer support is, let's just say, not very helpful.
So, if for no other reason than to give other people a quick answer to why their rates are incorrect, I think this is a useful question to have around.
In order to make the question less subjective, I've changed it from "why don't…" to "Can Magento be configured to use discounted rates without code-level changes?".
Best Answer
Looks like the answer to this is no. I had to go with code-level changes in order to get Fedex to use the ACCOUNT rates as opposed to the LIST rates.
Update: for reference here is the core code change that was needed.