You are probably running into the problem Quark has when the MAE Helper application is running. You can work around this problem by disabling MAE Helper using the following procedure (Note that while MAE Helper is disabled, X<->Mac cut & paste won't work):
1) Move MAE Helper out of the Extensions Folder
2) Restart MAE
3) Install Quark XPress
4) Move MAE Helper back into the Extensions Folder. Note that you have to
put it directly into Extensions by hand. Dragging the icon over the
System Folder won't put it in the right place because it's actually an
application rather than an "INIT".
5) Restart MAE and run Quark XPress
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