Stranger things have happened in Mach3 . Just correct the problem and move on.  MOST TIMES  things not staying changed are from not saving them after you have changed them. 

OR your saved directory got changed to read only.

Just a thought, (;-) TP

That still doesn't change the problem with the head plunging into the material.
And mine was not reversed.  But I did set it TO BE reversed and when starting a cut it now plunges UP

would something like this work with a gecko g540?  Or any other parallel port cnc machine?  I know the cable adapter doesnt work but would this?  If it does then I can test out different PC's to see if the PC is the problem.

Ok, may end up doing this: Order a ESS (Ethernet smooth stepper) breakout board, hook that up to my self built computer (I have 3 and I always build them to be super fast and durable) and see if this will solve my issues.  I have learned that a win 7 64 will not run a PP emulator expansion board and that the drive test program wont work with it either.  The PC I have been using is good, slow but good and I am sick on being locked into a parallel port trap.  ARTSOFT and Gecko need to cozy up and make a controller that runs of ethernet or USB and make it run for win 8 on down instead of locking people into limited options like so many others do.  If they can build a break out board to do this then you can build a controller with this built in and the software writers can write the code into the controller and the mach system and even send out an update.
As it is they are losing out on optional sales since others are building this stuff and making money on it.

Seriously...It's time
I lik the g540.  lets make it better folks!

there are a lot of different controllers that work with M3 ever pp, USB, Ethernet or pp to usb. gecko will change the g540 one day but there is a few controllers that you can just plug the G540 into to change it to USB or Ethernet. I have done it will be doing it again when computer dies on my machine with a G540.

you have something very wrong with your computer running M3 you may need to do a reinstall again make sure you get ride of the M3 folder nothing on the computer to do with M3 at all then do a reinstall.

I am going to be doing a computer change over to day with a computer with no issues with M3 from a computer that cant handle M3 very well at all the computer I am changing to is very old

On the pc that has been running m3 it was a "from scratch" PC.  It only had the software and programs that would run it and nothing else.  I reverted it back to that 2 times already.  (I am a computer tech...lol)  It was fresh and clean and had a program wipe it clean as well as search for related files.  It didnt help.  So I think it is just not willing to handle the system or the processes.  It is an old computer, not able to handle the OS thats on it very well but its what I had for a PP.
I am going to try the usb/PP cable offered by the same website that sells the smooth stepper and use one of my faster new machines.  It's one of the slower pc's I have and its a beast.  You would have to order a PC custome made to compete with it so I am sure it can handle anything thrown at it.

you hope not all computers can run M3 very well the one I am change is faster than the one I am replacing it with
what web site are you getting usb/pp cable from

http://www.cnc4pc.com/Store/osc/product_info.php?products_id=481
They have some good stuff there at decent rates.
I am going to build a large scale router/mill table and if this works out then I am going to use the same equipment to run it.

cool I get most of the stuff I need from http://www.automationtechnologiesinc.com/ they have most of the same stuff everyone else has a better prices and they dont charge stupid rates for shipping

NOW just a thought but the constant reversing Z axis reminds me of one of the setups Art used for licenses that had been abused. You may want to have the guys CHECK your license for you.

Just a thought, (;-) TP