Yes. Take a look at the "Sequence of Blended One-Axis Moves" example. You can put the Load Velocity and Load Accel in the loop to set different parameters for each target position.
LabVIEW example:
C:\Program Files\National Instruments\LabVIEW 6.1\examples\Motion\FlexMotion\One Axis.llb
VB and C examples:
C:\Program Files\National Instruments\Motion\FlexMotion\Examples
Regards,
Brent Runnels
Applications Engineer
National Instruments