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We study the effects of running coupling and gluon number fluctuations in the latest diffractive deep inelastic scattering data.It is found that the description of the data is improved once the running coupling and gluon number fluctuations are included with x2/d.o.f.=0.867,x2/d.o.f.=0.923 and x2/d.o.f.=0.878 for three different groups of experimental data.The values of diffusive coeffcient subtracted from the fit are smaller than the ones obtained by considering only the gluon number fluctuations in our previous studies.The smaller values of the diffusive coefficient are in agreement with the theoretical predictions,where the gluon number fluctuations are suppressed by the running coupling which leads to smaller values of the diffusive coeffcient.