It's odd, but some file transfers from certain USB devices through Aros on my laptop seem to perform the same. Though when I use the same devices on the OS3.1 A1200 there's no problem at all. I put it down to either the new, and not completely bug-free Aros version of Poseidon or the FAT/NTFS filesystem drivers. I doubt it's the hardware since transfers are fine through Linux and there's no way the Subway in an old A1200 is faster than a modern PC.
Both MorphOS and AROS practically share the same low-level driver (pciusb.device). There could be a bug, but without being reproducable and USB analyzer hardware (no longer have it), it would be hard to track down.