Wherever S.E. appears in the MCMC output, it refers to an estimate of the uncertainty in the estimate of the posterior mean that is attributable to the fact that that the posterior mean is calculated from a finite sample drawn from the posterior distribution. S.E. is estimated by the method of batch means. By default, 20 batches are used to estimate S.E.. To change the number of batches, click View → Options → MCMC.