Congrats for staying calm, analyzing the issue and fixing it.
Indeed, I think the CX/CM Boot2 3.1 is the only version which is not correctly supported by ControlX.
The included patches which make the Boot2 work in the ControlX context are compatible with all other Boot2 versions 3.0-4.4.
The problem is that, for some reason, the targeted code segments are very different in Boot2 3.1.
So indeed, a better/safer setup would be :
- to put Boot2 4.0.3 (the only version fully supported by ControlX) in the Diags/ExtnD partition
- in case the Diags/ExtnD partition gets erased/overwritten for some reason (it's very easy - just hold during a reset - this is a Boot1 combo, so sadly I cannot disable it), put a Boot2 image different than 3.1 in the Boot2 partition