The Allison never shifts quickly, IMO. However, they should be very smooth, especially stock. (Unless you have the power cranked way up, and even then...)
Sadly, that is the extent of my knowledge of the Allison. Hopefully someone will chime in with what could cause the intermittent smooth then rough shifts.
Oh, and mine shifts kind of hard once in a while when it is cold. I think that is fairly normal. Honestly, I'm not that impressed with the TCM they use. It tries to be smart when it should be dumb, and sometimes just messes up a shift randomly, but nails it perfectly the next time. Since you have a 2001, you could try loading a 2003 TCM OS (I believe you can do this), that might help some. The later OS's seemed to be better.