Helical Reconstruction

Hi,
I'm having difficulty getting a meaningful reconstruction of a 14-3 microtubule decorated with microtubule associated proteins (MAP) using the latest version of frealign. The reconstruction looks fine after the spider alignment and back projection, so I have good alignment and helical parameters. I've tried a number of different things in frealign including: number of subunits, starts, and beautify. As a test I've set the number of subunits to 1, FBEAUT to T, and changed the starts from 0 to 5 in increments. Only start 0 produces an image reconstruction with a seam in the microtubule. All other starts destroy the seam, symmetrize the density for the MAP, and produce density for the MAP where there shouldn't be any density. Any suggestions? Thanks.