It seems to be a common problem. I use Sonar 4 and the mixdown is intermittent and strange if "fastbounce" is enabled. If I uncheck it and mixdown in realtime then the mixdown goes perfectly. I don't know how it works in Cubase but I suspect that if you do the mixdown in a realtime mode it will work.
A lot of us are hoping that a future update will address this.
But for now I have a workaround. It's just slower.
Are you using your Pulsar 2 in the XTC-mode? This is a Creamware related issue. Only realtime processing is supported with the xtc mode (if I remember correctly the standard mode shouldn't affect audio export). It's the same situation with every other host as well. I have two computers and I bounce from my Creamware based DAW to my recording laptop through ADAT in realtime.