...yes that happens with Workbench 2.1 and 3.1 ROMS. I'm not sure how to solve this. You are having a right adventure with this A600! I bet you're getting frustrated now!
The problem is with the palette.ilbm file that's stored in ENVARC:SYS/
OS 3.x expects it in a slightly different format to OS 2.x
I had this problem when sharing the same files between my A1200 and A600