I use the multi-account version too and find it to be a great product for notifying me on both my Google Apps account for work and my personal Gmail account. Since Google doesn't allow you to use the username and password in the URL (which makes sense from a security perspective), I think a solution to this would be to just rely on the caching done by the user's web browser.
For example, the GmailNotifier.net app uses this URL for my regular Gmail account:
https://www.google.com/accounts/ServiceLoginAuth?service=mail&Email=my_email&Passwd=my_pass&continue=http://mail.google.com/mail/%23inbox
But, if you just type the following URL into the browser, you're automatically logged to your account due to the browser's caching and now viewing your inbox:
http://mail.google.com/mail
Similarly for a Google Apps account, instead of using this URL:
https://www.google.com/a/my_google_apps_domain.com/LoginAction2?service=mail&Email=my_email&Passwd=my_pass&null=Sign%20in&rm=false&continue=https://mail.google.com/a/my_google_apps_domain.com/%23inbox
Use this one and you're magically logged in.
https://mail.google.com/a/my_google_apps_domain.com
So, my question to you is, does your app store the URL in the registry or somewhere else where I can manually modify these URLs to their simpler versions? I did a find in the registry for the value "gmail" and didn't find these URLs anywhere. So, where are they saved? This might just be a quick fix, but it will work for me. Worst case scenario, the browser cache is cleared and you have to type in your creds again, which you have to do currently.
Thanks,
-- Damon