Here is the deal on 2001 OS and duramax issues.
During EFI-Live beta testing in 2005/2006 of which I was a part of it was discovered that some handheld tuners did not properly remove the speed limiters on the trucks and the return to stock option did not return the trucks to stock calibrations.
It was the biggest problems on 2001 trucks, in addition the 2001 computers are unique as far as the part numbers, they differ physically from the 2002-2004 LB7 computers.
It was found that the 2002 OS/15186006 was the best OS to use in all 2001/2002 trucks and for the last 7 years I have updated all of the 2001 trucks I have tuned to a 2002/15186006 OS.
I use only clean TIS files which have never been corrupted by a flash tuner.
So to answer your question it could be the OS, it could be a limp issue, low rail psi, etc.
If you want a clean/stock/OS just tell me your options for transfer case switching, electronic or manual and if you have a short or long bed and I will email you the correct stock file for your truck and you can start there.
Or you can purchase a tuned ecm with a switch from me and send the 2001 ecm back as a core.