While trying to troubleshoot what I thought was a Calibre issue, I found that using Kobo Utilities to delete all the covers and re-generating them on the device itself resulted in
all the colours getting the RGB values swapped. (It took me a while to figure out because the Aura HD is eInk and thus in greyscale).
It doesn't happen when I upload the covers...guess I'll be doing that. But is this normal behaviour?