I have had numerious problems with my 7344 since upgrading to the new Motion 6.0, and then Motion 6.1 firmware. For example, I have an encoder wired into an axis to read back the velocity (with no motor in the axis). This worked fine in the old version, but now is off by a factor of 2500. The problem exists in different machines with different 7344 cards, with different motors and encoders, so seems to be related to the new firmware.
By the way, Motion 6.0, and to some extent Motion 6.1, do not build correctly into applications in LabVIEW 7.0.