MT 643 is a 4 speed and 4th gear is 1.00:1 ratio, no overdrive. Only thing I can think of is the lockup torque converter isn't locking up. I don't have any direct experience with this behavior in an Allison but in my old GMC truck the torque converter stopped locking up when the transmission fluid was low and started foaming.
You might try driving it, getting the tranny up to temp and when you feel like it is being sluggish then pull over and check the diptick for both level and any signs of foaming.
There is quite a bit of documentation available for the MT 643 on the Allison web site available here
. Unfortunately, all the troubleshooting documentation, including a video, cost $$ to download.