Who has told you something has gone bad with Mach3 ?? - possibly someone who markets the Bob.
You must do a bit more detective work with a volt meter, before starting major re-boots. Having said that, you can install Mach3 again, without problems, but the only thing you would need to do is re-install the drivers.
However - more of that later.
The trouble with Bobs is that they interefere with the signals - in that they usually invert the voltage going to and from the computer. Lets start with the Z axis. There is a fault here - the led should be out, and light when you depress the switches, BUT at least it is working.
1. With the Bob connected to the computer, but not to the switches, check the outputs (i.e. the ones going to the computer) that correspond to the inputs from your switches and see what voltage they are - Ov of 5v. If you check the Z axis first and see what that is. then the X and the Y axis. They should all be the same. If not there is a problem with your Bob.
2. Go to Config/Ports and Pins/Inputs. First ensure that each input is enabled,and that all the Xs are shown on the same pin, all the Ys and all the Zs. check you have set the port number on them all, then check the active high/low. If the voltage on the Z axis is +5 then you should see that the "Active Low" button is not ticked - i.e. the computer recognises a high signal as the switch being tripped. If the voltage input is 0v then you should see that "Active Low" is ticked - i.e. the computer recognises a 0v signal as the switch being activated. (This is the wrong way round for correct working, but we will make a simple alteration later). If you check that the X and Y axis and set the "Active Low" to the same as the Z axis, you should now find that all the leds are now llit on the diagnostics board.
3. Check the voltage at the input of your Bob board on your three pins. Get a small length of wire, and, if the voltage at the Bob is 0v, then fasten one end of the wire to your 5 volt supply on the Bob and touch other end of the wire on the input. The leds should go out. (If the voltage on the Bob input is normally 5v then fasten the wire to 0v and do the same, the leds should go out.
4. If the leds are working correctly at this stage, then the problem is with your wiring. The Z axis is correct, so, before fastening it up, check the voltage on the end of the wire going to the Bob. Your X and Y axis should be the same, and they all should alter when you switch the switches. If they do, fasten them up.
On your diagnostics page, you should now have all the leds lit. Pres the switches and they should go out.
5. To make the switches work correctly, now go back to Config/Ports and Pins/Input and reverse the settings on the "Active Low" column. This should put out the leds, and they should come back on when the switches activate.
A bit long winded, but you can probably do it quicker that reading it. I have numbered the points, if you have a problem tell us where the thing breaks down.
Jim Pinder