Just to clarify, they found 1 particle of gun residue in it. Do you have any idea how small a particle is? It's microscopic.
I believe that if a gun (especially a recently fired gun) was in the toolbox there would be many more "particles"
My guess is that either a gun was in there, but a very long time ago (not related to this case) or someone that was around when a gun was fired put something in there and a particle was transferred.
However, I'm not gun residue expert. To reference this article:
"If the count is 2000+ on the face, hands, and other areas, your client has problems. Is the count 20 or less? An individual can get that by coming in contact with the police or other people." source: http://www.crime-scene-investigator.net/gsrstillviable.html