Router losing steps. Solution needed. Will this help?

[JAZZCNC]

The machine has rack & pinion drive to the x and y axes and 10x25 ballscrew to Z Y axis has 2 motors with the drivers connected to the same pulse/dir circuit.

This needs explaining better.? Do you mean your just using 1 Step and 1 Dir signal to drive borh drives.? This is a Big NO NO. One reason is the drives have resonance compensation circuitry built into them and doing this just confuses the drives so they don't know which drive to apply compensation too. The net result is that one drive/motor can get thrown into resonance. Then you have timing issues thrown into the mix and this just results in all sorts of random and strange happenings.!!

Not saying this is the problem but it certainly won't be helping any if it is setup this way.

Regards the R&P setup then what size are the pinions, ie diameter not No teeth.?
Reason I ask is because from the 0.01042 per step then that translates to 16.672 pitch with 1600MS and with a 5:1 ratio this means a pinion diameter of approx 83.5mm and this means a small pinion size.!
With Module size then pinion size for same number of teeth increases which means your module size would need to be small to have diameter of only 83mm And I'd be surprised if it's less than module 1 and more likely to be Mod 1.5 or even imperial.? . . . All this makes me wonder if your actually set correctly.?

Regards the Smooth stepper then it doesn't have any spindle speed control built into it or really any real I/O capabilty's that you would use directly so this means using with a BOB. It's main function is Motion control which it does very well.
Regards USB then I'd steer clear of using USB to power the BOB as it's unreliable and if it as the option to use external power then do so.

If you want the Best Motion control card for Mach3 then look at the Cslabs Csmio-IP-M or IP-S products which blow the others away. They also have Spindle speed control built into them. DONT use BOB so take away the biggest hassle in any control box and provide 24V I/O which connects directly to the Unit thru nice DIN rail mounted connectors so very neat and industry standard. (See pic.)