Hi @fjc100648!
This sounds remarkably similar to this thread which was running QIIME 2 in virtualbox. The ultimate conclusion was that virtualbox was mis-configured/not correctly supported for the CPU, as a Hyper-V installation worked fine on the same CPU.
That said, we super don’t understand what specifically triggers this, so all we know at this point is it has something to do with virtualization (apparently T2 and now T1 hypervisors, like ESXi, can cause it…).
Are you willing to help us debug this? I can see about creating some test situations and we can see when/where it actually breaks. No promises that it can actually be fixed however until we figure out what it is exactly.