OK, I think I know where we are now!
First, I think the speed controller you have is designed to get its pulse stream externally, and possibly also from an internal oscillator as an option. The latter is probably a 555 timer. An option to control the speed with an analogue voltage, which is the conventional approach, is not provided. So it expects to get a pulse stream with a variable mark:space ratio which it uses to switch the motor supply on and off. The frequency of this has to be pretty high, so you have to set the Mach 3 PWM base frequency rather high as well. But Mach 3 trades off base frequency against speed resolution, the normally expected base frequency is of the order of 25 Hz. I'm afraid that this makes the controller unsuitable for direct connection to the BoB which clearly just outputs the PWM from Mac directly. Whoever designed it didn't understand how Mach3 works.
It would be possible in principle to convert the Mach PWM signal at 25 Hz say to a voltage (it just needs an R and a C); then convert that back to a PWM signal at 2500 Hz; but all a bit of a faff.
What I would recommend is that you use a controller that expects to see a 0 - 10V signal, which can easily be derived from the normal PWM output using a normal base frequency. A possible unit is this one on eBay: 151151353460 I have one of these which I haven't yet used, but have seen good reports on them in other forums.
Then you will need a simple adapter circuit that smooths the PWM output to produce the 0-10V. I have posted a circuit somewhere in this forum recently.
Alternatively you can buy a board from Roy Harding at
http://www.diycnc.co.uk/html/spindle_boards.html - this one actually uses step/direction rather than PWM but it's just another Mach config option. Roy's documentation is good - you can download the manual. As this has reversing relays and things it is probably a good get.
Now, on to the wiring. It isn't correct to say that the signal is "negative going" as the BoB can only product 2 output levels, 0 v and ~+5V. The signal might be inverted, but that's a different thing. Almost certainly the motor controller expects to see a pulse train at 0 to 5V on pin 1 and ground (common) on pin 2. As you have shown the wiring pin 1 on the parallel port will be connected to the common on the motor controller. The resistor is there to pull up the parallel port output to 5V since normal TTL high level is only ~3V. I think it was right the first time. But frankly I would prefer to see some buffering between the parallel port pin 1 and the speed controller.
I hope this all helps - not the best news I fear.
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