That's to be expected, the feature is actually called "skip EFB Access to CPU" and when it's checked, that means that the EFB cannot be accessed by the CPU, meaning that some features in some games won't work, especially when the CPU is accessing various data from the GPU, I guess? Someone who programs on dolphin could probably give a more technical answer.
tl;dr - Skip EFB Access to CPU is a hack and breaks things.
tl;dr - Skip EFB Access to CPU is a hack and breaks things.