I have a Zenbot with 4 wire bipolar 285 ounce in nema 23 steppers. It worked great for a few months and then it started having problems it seems after I had disconnected the tower for a few days. The axes just bump and grind and bounce around, do not jog. I checked the mechanical, its all good. I replaced the ic drivers on the board, adjusted my configurations in the ports and pins many times, and got mixed results. Sometimes an axis would jog smooth, then another one would act up. I think the problem is between the pc and the driver now. Mabye my settings in the computer's device manager are not right. I'm using a Dell Optiplex tower with plenty of memory and gig.

Test with a volt meter at the parallel port. Put the meter between  a Dir pin and ground then jog the axis one way then the next and see if the volts go between 0 and 5 depending on the direction. You can do the same for the step pins ut its not so easy to see as the voltage change will be smaller but you should still see something. If that all checks out then it is outwith the computer that the problem lies.
Hood

I tested it. It looks fine. How do I open device manager screen and what do I need to look for? Thanks Hood

Not sure what you are meaning by device manager, if its windows device manager then there is no need to as the only thing you would need for Mach in there is the Port address. As you are getting the correct voltages out of the port then Mach has the correct address and your problem is further out than the computer. You could try increasing the Pulse widths to 5 on Motor tuning page or maybe even try Sherline mode as possibly your drives need a wider pulse.
Hood

I ran it fine for two months. 

Well unless somehow the pulse widths have changed it looks like you have problems with the hardware (Drives or BOB) could be something simple like loose connectors. As you have tested that the pulses are coming out of the computer then you need to look further out to the rest of your components.
Hood

I just replaced more parts in the driver, no good. Tomorrow a fresh 3 axis driver board will arrive from Mechatronics. My parallel port settings says it is working fine. When I try to jog using the xbox 360 controller, it just erratically bumps from one place to another. Sometimes even jogs in the opposite direction it's supposed to. The sound is very strange too. It's louder than before. If the new driver doesn't fix it, it has to be in the ports and pins configuration, right? Thank you for all your suggestions.

What Dell Optiplex tower are you using?
What velocity for the steppers are you are trying to run at?
Do you remember what the steppers sounded like when they ran?
( Did you hear anything like a clunk, clunk, clunk....sort of like hitting them with a little rubber mallet?)
Are you running off the motherboard PP or another PP?
Does that computer have on-board graphics?
RICH

I'll check it out in the morning, getting late now. Thank you Rich.

Here's why i ask. I have a GX520. I also use a SS with it with no problems. Suggest, if  you can, see what the quality of the PP signal is like using an oscilloscope , as it may have ringing on the signal and there nothing your going to do about it. Stepper velocity here with PP  is max 10 IPM and with SS have tested it to 120 ipm or so.
Not sure if it's the PC, as you said, worked great before.
RICH