As the war progressed, the major reason may have been broken lines of communication. Regularly required rolls and inspection reports were a lot of time and trouble. Anyone who has to file state, local and Federal tax reports, monthly, quarterly and annual, knows the required work involved to be onerous and unrewarding. If I could persuade my boss that our 941 might not to reach its destination, or that the folks who opened our mail them might not work for the government, there's a chance we'd delay filing until the situation improved.
The breakdown in Confederate chain of communications, especially west of the Mississippi, might have discouraged completion and processing of many military forms.