I have three accounts in the same window, I can switch which one I use currently by clicking on the email address. Two of them are Google Apps accounts, and one is a Gmail account.
It doesn't seem to work for me, I can only use my gmail accounts, those using custom domains don't have mail "enabled" but if I login to them alone they work fine. Maybe it's a problem at my end then!
When did you sign up for the google apps account? I've seen this issue with new google apps accounts because google now has all google app accounts also set up as a regular google account for other google services. For example - before if you had a google apps account for your business, but wanted to use a service like google voice - you had to sign in to google voice with a separate google account. Now Google Apps allows you to use your custom domain to sign into all google services. I've seen this conflict in setting up newer Google Apps accounts for customers because the Google Apps account is treated as traditional Google Account. I'm sure there has to be some sort of work around for this.
