Ok in that xml the limits are not enabled but presume that is just the xml before you actually enabled them or after you disabled them.
REgarding the probe, it may have been a problem if you had the X++ enabled as you have that set as the same pin.
Anyway it does sound like you have some serious noise there, hopefully screening will cure it but if not you may even have to go as far as adding caps to the inputs to suppress the noise.
The very first BOB and Drives I used were really bad and no matter what I tried I could not make them 100% reliable, after a lot of trying, even with caps and ferrites I gave up and went with Geckos and PMDX Bob and never had an issue again.
Hopefully you will get it with the screened and properly grounded cables though
Hood