I didn't see anything regarding ezdok camera keys not working when the ATC menu is open.
Since this is the FSDT GSX support forum so, I pointed out about the threads related to GSX and Ezdok camera together.
I know how to get around the GSX menu conflict but the ATC menu does not allow me to change views in ezdok when open.
Now it seems your question is entirely unrelated to GSX, and you have a problem with Ezdok camera keys not working with the ATC window, so you should really post this question on the appropriate forum.