It is not a software issue. The C31 needs to be activated a certain way in order for Whole Home to be activated on HR34/C31 installs. If the CSR knows what they are doing, it will be done correctly. For those that don't know, like the CSR in the OP's case, it causes issues.
I assume Shades comment about a fix coming is referring to a way that makes it easy for CSRs to do this.
Yes your probably right - the tech tried adding whole home to my account again last night also, just to see if it would work and he said it still wasn't working for whatever reason... so must wait for the engineers to fix this. I'm not sure why he mentioned a software update, but maybe he was meaning on there end?