Ive encountered this before.
I think it fixes itself after some updates, but unfortunately I cant recall exactly how I remedied it.
Also Ive only seen it occur under emulation. My a1200/ks3.1/40mhz '040 system never had the issue.
All I can say for sure is that AMOSPro does indeed work without this quirk (or can rather).
Also, do built in custom chipset based graphics commands even use graphics.lib? I think not.