Is there a setting that would override the location field on transactions? When a user changes the location on a sales order, it overrides it to the location set on the currently employees employee record (after submitting). I suspected a script or workflow, but am having trouble narrowing one down.

Does sound like a workflow or script. Did you check the scripted records? Customization > Scripting > Scripted Records > Sales Order

That's what i've been combing through yeah, was hoping for an easier answer, haha.