Ah, I didn't know that! All the more, a way to set Z3-RAM to 512MB on the A600GS would be extremely valued. 
On a 2nd thought... if this happens only on Amiga OS (regardless of running on A600GS, WinUAE or Amiberry) - but _not_ on Amibench, it's more likely an AmigaOS or Picasso96 problem? 
As far as I know, Amibench doesn't use picasso.
So could be a picasso issue. However, as Amiberry is largely based on WinUAE. It could still be a bug in WinUAE filtered down to Amiberry.