SmoothStepper. It's a USB device that acts as two parallel ports. It is meant to be dedicated hardware that would replace the parallel ports, eliminating timing issues caused by the Windows multitasking environment.
It comes with a Mach Plugin and a Windows driver. Mach talks to the plugin, the plugin talks to the driver, and the driver talks to the SmoothStepper, which talks to the breakout board and stepper drivers.
If you can find out what command language is used between the Mach Plugin and the Windows driver, then you could create your own interface layer between Matlab and the driver. Then you would not need Mach at all.
It's a tall order, but I gather from your post that you have programming skills. So maybe you can make it work.