Two things I can think of that might be the cause. The first is that you may have your settings setup to play the sound being encoded and since the encoding speed is different and may stutter, it could produce a rather bizarre sound. I don't have a current version of Cubase, but I'd look around the preferences for exports to see if there is anything about previewing the sound as it outputs and turn that off.
Another possibility is that the ASIO drivers for the ProFx16 are flaking out during the export and generating sounds that aren't actually being sent from the software, but rather just a bug. In this case, I'd try to see if there are newer drivers and possibly try using a different output (completely different sound card) while doing the export and see if the sound still occurs. That should help narrow the cause down.