I´m having this issue with the new 6.0.3.
Audio only no midi no VSTi.Cut,copy and move parts is almost impossible.
In my case gluing small audio parts into single long audio events reduces this problem.
Win 7 Ultimate 64
Cubase 6.0.3. 64
Do you have a bunch of editing already done, or is this happening on new projects. Bounce tracks after multiple cuts/fades and things will get smoother.