Thanks for your replies. Shutting off AFMA solved the problem, but as my 100L needed a +9 AFMA, not sure the overall solution will be satisfactory...Back to the original question:
If you're going to be doing macro that close, I'd suggest going to Live View so that the mirror is up when you take the photo. That kind of vibration can affect the results at that close of a focus distance. If you use Live View, then the AFMA isn't necessary for accurate focus.
THIS... let's get back to the question at hand. Live view is going to be your standard tool at that magnification anyway.
gripped 5DIII, 70-200 f/2.8L II, 24-70 f/2.8L II, 16-35 f/2.8L II, 8-15 f/4L, 50 f/1.2L, 85 f/1.2L II, 2x III, 3x 600EX-RT, ST-E3-RT