Hi. I have experienced similar problems with the Amicon filters previously. I found that using a swing bucket rather than a fixed angle centrifuge and keeping the speed at 4000 g, the recommended speed, resulted in better yields. If you have a large volume to concentrate (>12 mL), using an Amicon stirred pressure cell first may work better. This prevents repeated spinning of the filter, which is not recommended by the company. In my experience, using the same filter a few times is ok, but I guess that repeated centrifugation could eventually crack the filter.
Matt