Like shanelord said this is definitely an annoying problem. When I'm logged onto Google Reader (or any other Google service that Apps does not offer) using the account name I created based on my Google Apps e-mail, I can't click on the Mail link at the top. Because that link would assume I have a regular Gmail account and that's where it would take me. Then it would proceed to ask me to sign up for Gmail.
Same thing with Calendar and Docs.
If I use these services with Google Apps, the Google Account login should be smart enough to know that based on the e-mail address I used to sign up for it and direct to the right places.
But alas let's not divert from the OP. If a Google admin is watching this thread, would be nice to have a fix for the multiple calendar selection for Google Apps users.