Several recent studies have shown that positive (negative) phase of Equatorial Indian Ocean Oscillation (EQUINOO) is favourable (unfavourable) to the Indian summer monsoon. However, many ocean-atmosphere global coupled models, including the state-of-the-art Climate Forecast System (CFS) version 2 have difficulty in reproducing this link realistically. In this study, we analyze the retrospective forecasts by the CFS model for the period 1982-2010 with an objective to identify the reasons behind the failure of the model to simulate the observed links between Indian summer monsoon and EQUINOO. It is found that, in the model hindcasts, the rainfall in the core monsoon region was mainly due to westward propagating synoptic scale systems, that originated from the vicinity of the tropical convergence zone (TCZ). Our analysis shows that unlike in observations, in the CFS, majority of positive (negative) EQUINOO events are associated with El Niño (La Niña) events in the Pacific. In addition to this, there is a strong link between EQUINOO and Indian Ocean Dipole (IOD) in the model. We show that, during the negative phase of EQUINOO/IOD, northward propagating TCZs remained stationary over the Bay of Bengal for longer period compared to the positive phase of EQUINOO/IOD. As a result, compared to the positive phase of EQUINOO/IOD, during a negative phase of EQUINOO/IOD, more westward propagating synoptic scale systems originated from the vicinity of TCZ and moved on to the core monsoon region, which resulted in higher rainfall over this region in the CFS. We further show that frequent, though short-lived, westward propagating systems, generated near the vicinity of TCZ over the Bay moved onto the mainland were responsible for less number of break monsoon spells during the negative phase of EQUINOO/IOD in the model hindcasts. This study underlines the necessity for improving the skill of the coupled models, particularly CFS model, to simulate the links between EQUINOO/IOD and the Indian summer monsoon for reliable predictions of seasonal and intraseasonal variation of Indian summer monsoon rainfall.