ClassicWB 3.9 has by default Copper enabled!
Since Copper is an AGA related program, you should disabled it prior using it on your A2000.
One quick method without using WinUAE is by booting without Startup-Sequence using the Early Startup Menu and on command prompt issue:
1> cd C
1> execute Copper_disable
Just to be safe, you can disable a lot of components using the menu made by Bloodwych like Copper, StackAttack, BorderBlank, CyberBugFix, Fblit/Ftext, BlazeWCP, IconBeFast etc and then enable one at a time once your system boots succesfully