Regarding the ESS, I seem to recall when I start a machine that has an ESS or USB SS, then the DROs will display a random value. That does not matter to me because I have home switches and when I home the machine then the offset previously set will be correct.
I do not know how the ESS works if you do not home the machine so someone else would have to chime in on that or you could ask Greg on the Warp9 forum.
I am not sure what you are meaning about the limit switches. Normally you would daisy chain all switches together and use the NC contacts to do so. You would then set up the port and pin numbers in Mach for the limits. You can also set the home switches up to the same port and pin number if you wish, what would happen in that case is the limits would be treated as home switches when you ask Mach to RefAll. After the machine has homed the switches would then be seen as Limit switches again.
Yes if you are pressing RefAll and the axis only moves a short distance then sets Home, then it is almost certainly noise that is the problem.
Ideally you want all low volt signal wiring shielded and the shield correctly attached to ground at one end, all shields should terminate at a single earth point.
Setting some filtering for the home switches in the ESS plugin may help, do not set it too high or your switches may not be seen when they should, try maybe 5 or so and see if that helps.
Hood