I suspect the fuel. Try some yellow HEET. IFF you can get some, a pint of 95% Everclear will burn cleanly, too. (HEET is methanol which will start/prime a little easier. Everclear is ethanol, a little harder to get going, but will burn hotter once it is.)
Generally, water and alcohol will mix and not sputter. While water will not cause this when mixed with alcohol, other stuff can (sugars, gasoline-several parts, and, oils.) I also suspect that the stove’s ports are dirty/rimmed with brown. This can cut down on heat output. While it is possible to clean them out, be very careful. The aluminum is soft enough to be damaged. Many stove cleaners eat away at aluminum, too. If you made the stove, it might be easier to simply make another.