Simulation at Baseband or Passband
The only thing I could see, with the information you gave, is that the way you get from passband to baseband and vice-versa could affect your performances. It should not, but it could. 

Let's say you have to down sample to get to baseband, and up sample to do the contrary and you use filters to do so. If your filters have variations of 1dB in their passband and a cutoff frequency that cuts some of your baseband signal, then your performances could be deteriorated. In an ideal situation it should not, but some considerations (restriction on the number of coefficients of your filters, for example) may imply some performance degradation.