I added Seti@Home and World Community Grid to BOINC before registering BOINC BAM, but when I added two more projects in BAM, neither show up in my BOINC manager and I can't remove either of the original projects in BOINC or on the BAM website.

Any ideas what I'm doing wrong?

Did you attach BOINC Manager to use BAM? You also have to add your projects to BAM through the web interface, and then add them to a host or check the "add to host by default" box--if you wait to attach your host(s) until you've done that second part in the web interface, you'll save some time from having to add the projects manually later.

You should also check out the FAQ's:

http://boincstats.com/en/page/faq