All my stacked programs work fine... but there is a bit of a fuzz about the 1.1.4.9 OS... I can recommend trying these steps, in this order (that solved my problems with transposed layer B):
1. switch off and on REV2
2. enter service mode (hold transpose up and down plus global), choose to erase calibration data
3. go into global mode, and reset global data (don't forget to set these again to what you had them at, before the reset)
4. calibrate the osc/filter
5. calibrate the wheels
if that does not help, write support.