what is the chipset of the netmos pp card? i have found that some dont work, or the driver needs to be different.

The one from CNC4PC is a moshchip 9865 and another one I bought is 9805.

If you look in device manager at the ports properties it may say what mode it is in.

Easiest way to command the B axis would just go to MDI and G0B50 or whatever.
Hood

I manually actuated the b axis with the charge pump off but got no reaction.

The device manager calls out the motherboard port as Ecp printer port and the new one as pci ecp parallel port.  There are no other references to the mode setting. 

I measured the pin signal on the good port at 6.8khz and 1.6v when it was switch on in mach.  It was 0khz and 3.3v when switched off.  On the bad port i get 0hz always.  Im using cnc4pc's buffer board with a usb power source.  I measure 1.3v without this power source and 2.5v with it.  I used an external 5v supply and measured 3.2v at pin 16. 

Any ideas if this is a mach setting or hardware problem?

Have you swapped port cables around and also port addresses to see if the onboard port works the chargepump and B axis and whether the PCI one works the other axis and other chargepump?
Hood

yes.  I have swapped it around such that the onboard port makes the chargepump and B axis work on the second G540.

Well that would tell me there is nothing wrong with your Mach config but rather Windows is the issue. Just in case device manager is reporting the address wrong have a look from
Start
All Programmes
Accessories
System Tools
System Information
Components
Ports
Parallel



You should see the address there.
Hood

I will check that--thanks. 

Perhaps I should provide some detail on how I did the swap before we conclude that the problem is not with Mach setting.  I first swapped the cables, leaving everything else the same.  This showed that the bad port's cable works with the good port.  I also swapped G540s over between the ports, leaving all else in the original config, including the cables.  This showed that the good port is able to make the 2nd G540 work.

These two swaps narrowed down the problem to either the pci port, which could mean a physical problem with the card, the port, or a software problem in windows or in mach.

I'm trying to remember what happened when I swapped port addresses in mach (I've tried so many things over the past few days!) but I think when I did that, I couldn't get the 2nd port in mach (set to the onboard port's address) to work, but I'll need to confirm that.  Thanks!

I opened the system info program per your suggestion, to get the pci port address but I get the following error: Can't access the Windows Management Instrumentation software.  Windows management instrumentation files may be moved or missing.

I then swapped the port addresses in Mach and was able to make everything work with the original good set of hardware (onboard parallel port,G540,XYZA axis steppers) with the address in the 2nd port.  I then tested the inputs on the G540 by grounding them 1 at a time and looking at the LED indicators on the diagnostics tab of Mach.  I could make BOTH G540s show a signal in this manner.  I reversed the port addresses back to the original locations and repeated the input signal test with the same results.  So I knew I was getting communication through the PCI parallel port.  Still no charge pump signal on pin 16 though.  Finally I got the B axis working on the 2nd parallel port by disabling the charge pump manually.  I then could actuate it in mach manually.  I swear I tried this before but it it didn't work.  I added my C26 buffer board inline with this port and had to put the jumper on the pins to indicate that pins 2-9 are inputs (wouldn't work when they were set as outputs).  So, I still don't have a charge pump signal but I can make everything work by manually disabling this.  Any thoughts on why everything else would work and not this?

I suspect it is a problem between the PCI port and the G540, there have been many reports of issues with Chargepump and PCI cards. There are a few people that sell cards that will work, PMDX are one I think, I am sure they modified the card to make it work.
Hood