GSX UI window where you select Request boarding etc
That seems to confirm my suspicion that Ezdok is being confused by the different handling of standard menus ( the GSX menu IS a 100% standard menu ), which is handled differently in P3D.
But again, I don't have Ezdok, and I never used it, so that's just a guess, and since you are the only one reporting it (everybody else that posted here, confirmed they DO work together), it's not possible for me to say more.