Overloaded- Thanks for the troubleshooting suggestions.  We have had repeated success by turning the spindle off during the "in air" run.  No phantom limit switch errors when the spindle is off. 

Do you think switching out the proximity sensors for a physical switch would solve the problem?  Is there something else we can do instead of having to change those out?

I appreciate the ideas!

Is there an inverter/VFD ?

You mentioned 0.01mF caps. were installed.
I'd reinstall 0.1mF caps, check/reroute the limit wires well away from any high voltage lines, connect the shields only at one end (in the control box), make sure the enclosure and machine is properly grounded.
Noise can be a pickle to track down/isolate.
Checking motor housing and frame members to a good ground with a meter while running will sometimes surprise you (me).

We do have a VFD

Noisy buggers they are, most of em'.

I wired the .1mF caps in there.  When reffing home the proximity sensors will light up but not stop the jogging.  I tried to run a simple program anyhow but the phantom limit switch still triggered.  

Definitely noise somewhere so we will be continuing on the list of ideas that are in here.

Hi Coach,
  You mention "Limit Switches" and "Proximity Sensors".

Which do you have .... and where ?

The indicator on a prox. does not necessarily  mean that it is seen by Mach3.
Trigger all of your switches/sensors while observing their associated leds in the Diagnostics screen.

We tested all of the motors and grounds for the machine which have continuity.  The CAP's are removed now and the limit switches work.  We are still experiencing a "limit switch triggered" almost half way through the program. 

We detached the proximity sensors from the machine and tried to run the program to see if vibrations were causing the limit switches to be triggered, it did not work.  The "limit switch triggered" message came up again during the process. 

This discussion has now moved here http://www.machsupport.com/forum/index.php/topic,32178.0.html

Tweakie.