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What windows version are you running Peter?
I run BYEOS and EOS utility side by side at times and never had an issue. I run a Win7 64 Bit.
When I plug in my DSLR and power it up, the EOS utility opens up, but I can just let it sit idle and open up BYEOS. Then I can choose to hover over the EOS utility and close it using the X button on the top right hand corner of the icon.
Bo
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