Yes it's a strange one. I have tried a lot of differing versions of E-UAE, JIT, normal, G5 specific, and they all do the same thing. I thought it may have been my machine, but every other sound on the system is fine. I have tried to fine tune the settings in E-UAE, with no improvement.
Lucky, I do have some real Amigas setup.
Running MorphOS on a Power Mac Dual G5 and a Mac Mini G4.