OK I have fixed this by uninstalling and re-installing Modify ePub. I guess something went wrong when I installed it at the same time as Quality Check. I notice this time it defaulted to both "Add to main toolbar" and "Add to main toolbar when a device is connected". The first time it defaulted to "Add to main toolbar" only, which is what I used. (Wording of options may be slighly wrong).
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