Back in the old days when I ran GPUs that was always a problem in mixed systems when running the same project. Back then the only solution was what you are doing. I found it easier to run 2 different project with the GPUs so that I didn't have to babysit the computers.

Things may have changed ... then again they may be the same. I believe the problem was with the BOINC scheduler not asking for the correct type of WU.