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This communication evaluates the mechanisms associated with the inherent difficulty of global coupled ocean-atmosphere models to simulate the thermal vertical structure of the equatorial Atlantic. The study is done with use of the coupled GCM developed at CPTEC, which consists of CPTECs global atmosphere model fully coupled over the global tropics (40S-40N) with GFDLs MOM3 ocean GCM. Coupled and uncoupled simulations were calculated in ensemble mode, with ten members runs, 8 months long each starting at every calendar month for the period 1982-2001. Systematic differences between simulations done with the CGCM and OGCM forced with prescribed atmospheric fluxes, as well as against PIRATA array data over the tropical Atlantic are used to argue that the systematic errors of the coupled model over the equatorial Atlantic can be separable into a surface and under-thermocline ones. Evidences are shown to suggest that surface temperature systematic errors are attributable to insufficiencies on AGCM stratus parameterization, which generated excess solar radiation over the regions of stratus decks over cold waters along the southwestern coast of Africa. For the under-thermocline processes, however, it is shown a remarkable locking to the seasonal cycle, with systematic errors maximum amplitude occurring in April/May, regardless of the month of model initialization. Linkages to AGCM rainfall deficiencies over the equatorial landmasses are speculated.