The BOINC manager always uses the last set of preferences that were created, no matter where they were created (BAM! or any project).
You can probably solve it by going to your BAM! preferences, edit them (no need for making changes) and save them. This will update the last update time and should make your manager use BAM!'s prefs again.
I tried EVERYTHING I can think of, done that lots of times. All I can think of is that somehow AQUA and BAM! is still communicating OR AQUA made a enrty somewere on the PC's to somehow get AQUA's settings and NOT BAM!.
To be a little bit more clear on the matter. When BOINC synchrosises with BAM I can open the prefs file and DO see it's using the boincstats.xxxxx.xx.xx, but just after that when BOINC finished with the sync, I go and open the same file, and guess what, AQUA is BACK AGAIN!!! I wnated to crakc!! I can't see how those STUPID settings can get back into the file.
I'm a beta tester for a few companies, So I can send you reports or whatever you need to show you what's happening.
Here is a part of the settings file. It JUST went back to that after deleting th file and sync-ing again:
<global_preferences>
<source_project>http://aqua.dwavesys.com/</source_project>
<source_scheduler>http://aqua.dwavesys.com/aqua_cgi/cgi</source_scheduler>
<mod_time>1273424703</mod_time>
<run_on_batteries>0</run_on_batteries>
<run_if_user_active>1</run_if_user_active>
<run_gpu_if_user_active>0</run_gpu_if_user_active>
<idle_time_to_run>3.0</idle_time_to_run>