First click the measure button on the configuration control to measure the resonant scanner frequency. This helps improve the accuracy of the frame period estimate.
If you still have problems, try reducing the volume period adjustment on the Fast Z control. The default is -600us. Try -1ms.
This is designed to account for jitter in the resonant mirror frequency that can cause missed triggers, which creates the sync problem with the piezo control.
Useful ScanImage Links: