The bobbin friction stir welding (BFSW) process has benefits for welding aluminium alloy 6082-T6 in the boat-building industry. However this alloy is difficult to weld in the thin state. There are a large number of process variables and covert situational factors that affect weld quality. This paper investigates how tool holder and machine-type affect BFSW weld quality of 4 mm Al6082-T6. The variables were tool features (three types), machine-controller type (two types), and tool holder (fixed versus floating). Fourier analysis was performed on motor spindle current to determine the frequency response of the machine. An interaction was found between the computer numerical control (CNC), the degrees of freedom of the tool holder, and the substrate (workpiece). The conventional idea that the welding tool has a semisteady interaction with the substrate is not supported. Instead the interaction is highly dynamic, and this materially affects the weld quality. Specific vibrational interactions are associated with poor welding. The CNC machine-type also emerges as a neglected variable that needs to be given attention in the selection of process parameters. Although compliance in the tool holder might seem useful, it is shown to have negative consequences as it introduces tool positioning problems.