I have been having this problem for a long time:
I have brokerage and banking accounts at e*Trade, and both of them are accessed with the same userID and password.
The brokerage accounts update correctly, and apparently DO NOT require me to enter the 2 factor authentication code, and always update correctly. The E*Trade Bank accounts, however, DO require the 2 factor code, but Quicken often (almost always) does not ask me for the code on the first try, and instead returns a CC-503 error. I then have to update again, and on the second try it ALWAYS asks for the code, and the update works correctly. I wish this bug could be fixed.