There's nothing wrong with post-rounding, however setting lb(i)=ub(i)=0 for the appropriate variables should force them to an exact value of zero.
Of course, since you know the variables are zero, an even better approach would be to not include them in the list of unknowns in the first place. Possibly, quadprog will pre-process the problem this way for you when it sees that lb(i)=ub(i)=0, but I'm not completely sure.
