Is there a way to actually see or determine how many pulses my PC is achieveing at the parallel port?  I'd like to compare various PC configurations so that I can get the max 45khz.
Thanks,
-Neil.

You set the pulses on the config port page. You have to restart Mach each time you change this. You can see what the pulse numbers are live on the diagnostics page in Mach. When you run a driver test, you can see which setting will give you the smoothest wave.

I have seen it not saving a lot of different things lately. Not saving the emergency stop pin settings and so forth.
I wonder myself what could be causing this.

You need to have a license to run more then 25KHz... If you change it the next time you open the software it will be set back down to 25KHz.

Thanks
Brian

That makes sense. Perhaps that is why I haven't noticed this for the frequency.
Any idea why emergency pin settings don't stick? To be more precise, not only do the pin numbers not always save on the Estop, but once you click an estop as active in the settings, you can't save it as turned off. Rather I wasn't able to.

I paid for a license so that I can unlimited number of g-code lines, and thought that was the full registration. Is there a separate license for just the frequency?

That should be it Drstein99,  make sure that when you click 'Help>About. that it shows registered to your name,. if it lets you do more than 1k lines it should be ok, but check.  Also, the frequency changes back to 25k if there has been an error.   I assume you have an not too old comp with available processor and mem.    Change freq to 35 and see if it will stay at that.   
and ofcourse the all time favorite response to software problems...   upgrade to latest version. or if already did , then re-install.   
btw, if brian or anyone else tells you different , then I do what they say 
good luck,
Paul

Paul is correct, there is no separate license file for the frequency setting. The rule of thumb for the frequency: If your velocity slider is all the way maxed, move up to the next highest frequency setting. If you are only of capable of 22khz on your hardware 45khz will not do anything but take away processor cycles.

Leeway. Sometimes mach can be a little strange on inputing numbers. Make sure after you enter a value be sure to hit return or apply if it is there. I have done the same thing entering a number hitting ok and mach didn't save it..

Chad