The in kernel ixgbe driver does not have IEEE1588 support yet. We are working on doing that enablement but it's not released yet. So I'm assuming that you are adding this support yourself? Also, since 1588 support is in the 2.6.38 kernel already there is no need to use the ptpd. Please look at this link which explains how this works in teh new kenrel:
We will be adding the 1588 HW acceleration support to the ixgbe driver in the near future.