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.