Thanks @abctax55, you're spot on. 
In order to conform with Federal and state agency requirements, we are unable to make blanket program changes to allow negative numbers on all input fields.

However, we can look on a case-by-case basis at selected input fields within the software to determine if changes could be made which do not conflict with either Federal and/or state requirements for both print and electronic filing. 

In order to review these specific sections, please provide the following information on this thread Supporting Detail doesn't allow negative numbers per line:
-Tax module (Individual, Partnership, etc.)
-Agency (Federal) (State)
-Screen Number
-Input field Description
-Code Number.