Download the MCP package from Aminet and install just the mcpramlibpatch in your startup-sequence.
You can also try to install blizkick with its romfixes module, (you could try SystemPatch too) although i don't think that this will help with OS3.9 .
Try a newer/different version of the 68060.library.
If all these doesn't help, open your Amiga and clean it up.