I just stumbled onto something odd. I had forgotten that my main host has its own preferences. I tried to turn them off thinking that my web preferences with BAM! would take over. So, I unchecked the "I want to customize my preferences" box and then unchecked the "Use GPU while computer is in use" box. Then I checked, and sure enough, my GPU stopped. I cleared the dialog (hit the clear button) to return to my web settings, but the GPU still would not run.

So, I can run the GPU while my GPU preference is checked, but as soon as I uncheck that box, it stops. So my BAM! preferences tell my host to run the GPU, but when I clear my host preferences, my host preferences still take preference over my global BAM! settings. Any ideas?

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If the last change you made is local, that will take preference!
Change your BAM settings and update a Boinc Project.