You might not take into account all noise contributions. Try setting the maxsideband parameter to a large value (see also section 2.2.1 of
http://www.designers-guide.org/Analysis/sc-filters.pdf) or use the fullspectrum option (only available in APS) together with a suitable value of the maxacfreq parameter.
I would expect roughly the same noise and jitter for both of your cases (if the average noise is not dominated by the noise during the signal transition and if the signal slope at the transition is the same in both cases). However, if you use the same value of the maxsideband parameter, the maximum frequency of the noise you take into account in case 2 is only half the value of that in case 1.
You might also want to ask your question at
http://www.cadence.com/community/forums/33.aspx or contact Cadence support if this does not solve your problem.