Looking at your vi is a little difficult without comments (in the block diagram), but I will try to make some comments.
One thing I noticed is that the Out Port.vi is supposed to have a 16 bit number entered in it, is there a reason that you are converting all of the numbers to U8??
It seems that you could create 2 subvis. One would handle the calulations and configuration for acutator 1 and the other for actuator 2. That would just entail you copying/selecting your sequence structure and adding a second set of controls for actuator 2 (frequency and duty cycle). That way you could have the time delay be independent for each subvi.
I will try to modify your vi later today if you cannot get it to work and will post the vi if you need it.
Kenny
Kenny