||Yeah, that's also an indicator of a line pressure problem.
The real test is to hook up sopem pressure gauges at the 3rd gear clutch port and see if you have the right pressure in 3rd gear, but I think you may have found something important: when you set the shift valve manually, you are bypassing the accumulator valve in the valve body. If this sticks (which is common in *ALL* transmissions) then you'd have an issue like this.
From here, I'd say contact Allison and get some manuals on your tranny and see what controls line pressure and how to check it. I'm not familiar enough with this trans to give you specific troubleshooting tips from here.