Unless someone else has suggestions on other things to try, or on how to debug this, I'm not sure what to do next (other than test with the motherboard's serial port when my cable shows up).
I'd be highly interested in the behavior of the onboard connector, as well as that of a USB-to-serial port if you happen to have one you could try.
We could also try artificially slowing down the Icom programming loop if you want, which might mirror the behavior of the VM. However, I think I'd prefer not to commit that and slow everyone else down, since you're the first person I've ever heard about with this problem. Still, at 9600 baud (non-hispeed mode) it surely seems like it'd be hard to push it too hard.
Out of curiosity, does dmesg indicate that they're 16550A ports, 8250, or what?