this is what I found out
working in the port and pins....input

with X- active high
the x axis works good but not y

with y home off de active x axis will not worl
with y- off de active x axis works but not y

when i deactive any combination of

with y- deactive
with y home de acitve x will not work

with y- deactive
with y home deactive   y will not work either

with x- active high
everything works except y

I did have z and x working but y moving run direction
but, I could not duplicate this again

I hope this makes sense I got so confusedI had to write it down

Also when I turn off active low on both
x- and x home

y axis moves away from home switch

yellow light go out in M1 limits and m1 home diagnostic screen

and red overlimit led is now out on setting screen

I am not sure I am understanding what you have written but if I am it does not make sense at all
Changing the active state on one limit should have no effect on another unless they are not wired as you have the pins set.
Is there any chance you can trace the wiring from each switch and see where they go to on the breajout board?

Hood

before I start tearing this thing apart I have loaded Mach 3 demo
and my machines xml file ona Gateway running Win7 last nite....it did not run....
it was late and I quit....
I am going to spend some time trying to get Win7 to run
perhaps I got a problem at the parallel port...I noticed all
my led lights were not all lit green like they were on the diagnostic
page of the Win7 computer....just a thought.....I thought I remember
seeing a row of green lights all lit up before and now there is one out....

If I can get a screen shot on here I will send you one of the
diagnostic page to show you what I mean....

also, if I can not get the win7 to run mach3 in short order
I will go back to the XP computer and I will take the top
off that controller and see exactly how the wires are running
to breakout board for the axis motors....take a pic
It should be easy to see the way they are cabled...there is only
three of those magnetic switches on the machine and they share
the limit and home switch...Mach three somehow knows what the limits
are based on the configurations of the home switch....I think this is the way it is??

Okay here is the latest:
I could not get win7 to run everything looked good
I verified the com port address it is a 32 bit processor
so I quit with that after an hour...

I went back to the XP fresh this morning
I left ports and pins alone
I left just the way they were given in XML file
which was:  X- and X home enabled and active lows for each
the same for all the axis enabled and active lows enabled

I then went to Homing and limits screen
x axis I reversed with home negative off
y axis I reversed with home neg checked on
z axis off with home negative off

the machine now homes and zero's out
and the machine now jogs at the right speed

before when all this was going on the thing was
just dragging in speed at jog
but now it has the right jog speed

Hood, I know you were following this at one time
what do you think is going on here
I never did take the cover off that controller
they used some kind of crazy screw with an uncommon head
I am not sure what kind of wrench is needed to take if off
it's not torx, not hex.....

If it was intended for a user to be able to change a fuse maybe sometime...
looks like they would have used a common phillips or something just for an access

anyway it is homing
but, I don't really understand???

sorry for the long email......

I have never used W7, not keen on it but looks like it may have had some sort of corruption or the driver was not being allowed to work correctly.
As long as its all working now then all is good
Hood

Yeah!
I wasn't in a big hurry to switch to win 7
I like XP just fine....switch to Apple
just about the time Vista came out
don't have any experience with Vista either....

I want to thank you for helping me out on
this.....

Vista lasted 2 mins on my computer, went back to XP. Have a laptop with W7 and I would format it  and shove XP on but the boss wont let me as she likes some of the games on W7
Hood

hey let me ask...
why do I not have the cross hairs showing on my table display
like the support video shows....when a program is loaded according
to the video should be able to see the yellow lines representing the
x and y axis moving across the table display as you jog the machine

I have the soft limits set and the machine homed.....

I have watched the video several times must be missing something