The sentence could be written like this, 'The Pulse Speed switch controls the output pulse speed and the machine's behaviour.'

If it referring to pulse speed, then it should be written 'The Pulse Speed switch controls the output pulse speed and its behaviour'

The sentence as written is ambiguous, and I do not think earlier answerers' 100% confidence levels are justified.
Perfectly plausible readings (in the obsence of context) include: "The Pulse Speed switch controls the pulse speed and the behaviour of the output of the machine" and "The Pulse Speed switch controls the speed and gehaviour of the machine output pulse".

Under the assumption that the pulse speed switch controls are part of the machine, then there should be no question about what is effected by the switch -- both the pulse speed and the behaviour of the machine.

Would it not be strange, if the output (pulse speed) of the machine did not affect its behaviour.

The phrase would make more sense if it refers to the behaviour of the machine, the problem is the absence of the definite article "the" before behaviour, so if the phrase is expanded literaly it would be rewritten as "... controls the output pulse speed and the output pulse behaviour of the machine". So by looking purely at the sentence structure, the world behaviour would relate to the output pulse (not the output pulse speed).

Of course it is possible that the sentence is just poorly written and the author meant "... controls the output pulse speed and the behaviour of the machine". Here behaviour would clearly relate to the machine, and would make more sense.

Alaa