The difference lies in the presence of a heteroatom in the ring and in the carbonyls instead of alkenes for exocyclic bonds. Both of these stabilize the localization of the electrons in the anti-aromatic state rather than the delocalization of the aromatic state. The resonance structures placing one exocyclic pi-bond electron within the ring are carbon radical structures, which are more stable than an oxygen radical structure as required for a carbonyl.
Janicki and Patelli demonstrated the effect of a heteroatom stabilizing the localizations of electrons in terms of spin splitting - Janicki, Slawomir Z.; Petillo, Peter A., Journal of Physical Chemistry A (2000), 104(35), 8224-8226.
As for the maleimide paper, the authors point out that the destabilization is very small even for those systems, and that their calculations aren't always consistent. In particular, comparison with the acyclic system shows an unexpected stabilization rather than the slight destabilization. In any case, they point out the the measured destabilization is much less than anticipated by reactivity under Diels-Alder conditions.