FWIW.
There is nothing on the BO support site about Import Wizard problems with shortcust, but there is a reference to user prefs not being imported correctly. That issue is addressed in a hot fix, which I downloaded and installed. (You can install just the wizard upgrade if you don't need the other fixes.)
I also rebuilt the APS datasource through the CCM and painstakingly double-checked all options and settings between the old and new components on the CMC. Then I logged out of all CE applications on the new server before re-running the Import Wizard.
This seemed to be more effective than previous attempts. Only one recurring schedule failed to import. A few shortcuts also failed again, but one was for an Excel format . The others were for references to objects that could not be found on the source server. Which raises an interesting observation about CE: That an object can be removed but its dependent shortcuts are not affected.