So, after I installed my HDZ, I didn't encounter any issues. I cut and drilled a spoilboard, and surfaced a piece of MDF multiple times while tramming the router. I then replaced my computer. I don't think that should have had an impact, it's pretty straightforward, just a Windows 10 machine running CNCJs, with same settings, and both machines only had Carbide Motion as another application installed (for the driver). I was using a laptop but the small screen resolution and bad trackpad were really annoying. Anyway....
Then I tried to surface my actual spoilboard. Same thing each time I ran the facing operation: router goes up to Z home, then the program throws an error about hitting the soft limit. As I mentioned, this is in CNCjs. I then have to reset and unlock.
Now to think about it, I'm not sure if I had activated the soft limits before or after my initial successful operations. I think it was before, right after I setup the HDZ, but I'm not 100% sure.
In any case, it's happening now. I then saw the part about switching the post-processor in Fusion 360 so I setup the Strooom (I was using the Carbide3D one before). The same error happened, except with this processor it happens about 10mm lower than before on the Z axis. I did get that warning about the WCS system. I tried without and with setting that WCS offset to 1. I have no idea if that is right, it wasn't needed before and I don't yet understand its purpose.
In order to be able to continue, I had to deactivate the soft limits. Without those, it seems to work fine.
Any ideas? Should the soft limits remain disabled? Maybe that's only for UGS?