Most my projects currently are doing work even after I synchronized with BAM!, but aren't listed as connected or in my project list. I double-checked they all have the same email address and password as here. As for username, it's not clear... when I'm running BOINC, some projects list my email user from user@host, and some list my real name... I don't recall ever being able to enter that, didn't they just all make it up and I have no control over username?

Did you attach those projects manually? If you want them to be in the account manager, you'll have to add them through the website.