It appears he applied for and attained a pension while a resident of Arkansas, Confederate pensions were issued from the state they were residing at the time, irrespective of the state servied

Confederate Pension Records, 1891-1935 No Image

Name: Joseph B. James
Residence Location: Independence, Arkansas
State Served From: Alabama
Division: Cavalry
Company: E
Regiment: Independence ?????????
Vet Application Year: 1906
Comments: approved

https://www.ancestry.com/search/categories/mil_pension/?name=Joseph+Berry_James&military=_tennessee-usa_45&residence=_Franklin+County-Tennessee