I don't recall what all goes through the AXSBOB board besides the encoder, or if the CIB has one. It sounds central to feedback cross talk. Run away is common to tach feedback.
If the issues were local to one axis, you may be able to change the order of homing to isolate which is causing the others to freak out.
One faulty encoder or other component in the feedback path can brown out the supplies to the rest of the system, causing all kinds of unrelated conditions.