After banging my head against the MSDN documentation* for a few days, it turns out that TrackPopupMenu and TrackPopupMenuEx (in CE 5.0 the former maps to the latter) are not in Menu.lib as per the documentation but in Coredll.lib.
Also causing problems was the macro redefining TrackPopupMenu to TrackPopupMenuEx was not working due to I believe Afx.h, so I just manually swapped to using the Ex function.
*MSDN url: ms-help://MS.WINCE.v50.en/wceshellui5/html/wce50lrfTrackPopupMenu.htm