What is the advantage of using a motion controller rather than just a PC and BOB?

[Neale]

As said, a motion controller takes the pulse generation task away from the PC. Mach3 and LCNC both have to go to considerable lengths to try to persuade an operating system that is used to doing its own thing to produce a regularly spaced pulse train to drive, particularly, the step signal. The pulse rates needed can get close to limits of the PC and sometimes beyond, as you have seen. The MC takes on the pulse generation role and by using dedicated hardware will outperform a PC. The PC and parallel port are OK up to a point but have their limits. Of course, an increasing problem these days is that most new PCs don't even have a parallel port so a motion controller that connects via USB (good) or Ethernet (better) is almost essential. Add the fact that Mach3 needs a 32-bit version of Windows to use the parallel port and again a new PC will come with 64-bit Windows 10 and you are stuck.

A parallel port limits you to 5 inputs for limit switches and so on. This is a physical limit of the parallel port - that's how many pins will accept input signals. There is also a limit to the number of output pins. A MC can have many more input and output pins to get past these limits. Generally you will specify these using the ports and pins page in Mach3 - my CSMIO/IP-M uses port 10, for example.

Mach3 works just as it usually does but passes movement instructions to the MC to turn into step signals so it has a lot less to do. It will send a buffer-full of data, so if it gets distracted by some internal housekeeping task, the MC will still have data to get on with until the PC catches up again.

There are motion controllers that will work with LCNC but as far as I know, there are no MCs that will work with both.

There can be other benefits - some motion controllers will use 24V signalling for better noise rejection (more reliable), and differential signalling (for the same reason). Ethernet is generally a bit more reliable than USB - better ground isolation and differential signalling. Again, this is for noise rejection - a CNC control box is electrically quite a noisy place.