OK
 3.3v could be your problem, older ports were 5V but newer ones can be lower such as your 3.3v. Some breakout boards casn handle this others can't, also noise can be a problem the lower the voltage is as any noise can make the difference between Hi and Lo blurred.
 As however you can use the other CNC control software then this may not be the case.

The voltage you are seeing on the Step pin is good, doesnt matter what it is as your meter wont be able to keep up as its switching fast between 5v and 0v, or in your case 3.3v.

You could try with  a PCI parallel port as they tend to be 5v although choice can be dodgy as some are, well shall we say crap
Where are in the world? If the USA try www.rogermachine.net  Ron sells PCI Cards that are known to work well with Mach. I am in the UK but have bought cards from eBay and had good luck with everyone I have had but others have posted in the past that the ones they got were no use.

I will try and find some data on your breakout and see if I can find anything.

Hood

Ok found your board, its a combined axis drive breakout baord. Dont see any problem at first glance but maybe try setting up all of your axis step and direction pins as active low. I have never seen a problem with having them either Hi or Lo or a mix but Chip has often mentioned that some drives are particular about the state so it may be worth trying that.
Hood

So I er... found the problem...
My PSU did not have enough muscle to push the motors. I have a "Logic Power state" led in the circuit that shows when theres power on the IC's. My test equipment (a row of LEDs) used for marking the sequence from the motor out connections obviously requires WAY less power than the actual steppers.

I found that by ripping two old computer PSU's and bridging them for 24V worked a chink! Sweet actions left and right. I wonder if the pulsing had something to do with this issue since the other software packages work just fine. Anywayz, after some time on the motor tuning screen I FINALLY got my rig to move.

Thanks for ALL your help Hood. BTW I downloaded a layout screen I think you made from the Mach website, cool stuff man!

Good you are going now.
Keep your eyes peeled on eBay for a toroidal transformer, a suitable capacitor and a rectifier and make your own power supply. Not sure about your drives but I know Gecko says that switch mode PSU are not recommended for their drives, much better to have an unregulated power supply with the traditional transformer and smoothing capacitor, better check with your drives first though just in case they recommend a switchmode PSU.
 As for your other software driving things, could be your drives require a longer pulse, also what kind of speeds were you getting from the other software, maybe Mach just gives you more so the drives are requiring more power.
 Main thing is you are up and running
Hood