Clocking conflict with Boom and Apogee Duet

Hi all
I enjoy Boom 2. It has helped me tune my monitors and dialed out some harsh resonant frequencies. I'm having a problem though:
I mix music on pro tools. I want to keep boom on because otherwise I invariably mix out some frequencies that my monitors create too much of. The problem lies in the clocking, when I rout pro tools IO into Boom 2 I get all these clicks and pops. I understand this to be a 'clocking issue' where my interface and boom both want to do the same job. How can I let my Duet's interface override the clock on Boom 2? In all honesty I'll be rather surprised if anyone has an answer as I feel this is something you can't actually do and I may need to find a different way to EQ my monitors. 
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