Looking at your Bob manual it states it has a 1k load resistor built in. Also have a look at the RHS image at figure 4.
I don't know what voltage the hall effect sensor is being fed, but if it's 12v, then across a 1kohm load that is 12mA.... In reality it will be less than this because of the forward volt drop across the optocoupler... You may need an additional parallel resistance across the two pins of the optocouplor and the resistor ..... Depends on the spec of the hall effect sensor what load it is expecting to see...
https://www.google.com/url?sa=t&source= ... J5825jgd4RAgain..... A scope will clear everything up.
Measure the output out of the sensor and also the lpt port pin from the Bob to the UC motion controller too.... So you can see exactly what the Bob is getting.
Try to run it at a low medium and high rpm with some stability (not sure how you are controlling it but you just want it running at a fixed speed (no uccnc pwm input)