+1 to Herb (Guitarhacker) - not sure why you need to export those midi parts seperately

I started out doing the mixing in Audition 3 several years ago and just continued doing it in Sonar. I will try doing it in the same project and seeing how that goes. I guess I am still scratching my head over why installing a "better" audio interface would suddenly cause this to happen. I never even thought about an issue like this before... the imported audio always synced up flawlessly. I'll let you know how it works not exporting the audio.

Well sadly the same thing happens. The problem is in the rendering process. And again sadly it is a Cakewalk issue because I tried it in Ableton Live 8 trial and it is syncing up perfectly. Urrrgghhh. I guess I'll be working in Ableton for a while.  I like it ok but Sonar is better for me. I wish Cakewalk support would get back to me. Oh well... at least it's not a complete loss. 
If anyone comes up with a solution please let me know.

have you tried freezing the synth tracks?

I freeze the tracks to render the audio and then I export them. I just froze the synth tracks this last time and tried playing them back without exporting. The bass was way ahead of the drums. The problem is in the rendering. I tried to using the manual offset and that didn't help at all.