ixgbe: Fix PTP X540 SDP alignment code for PPS signal

This patch fixes a bug in the method used for calculating the trigger
alignment for SDP0 when enabling a PPS output on the X540. The alignment math
wasn't properly taking into account the overflow cyclecounter, and was
misaligning the pin triggers so that two X540 devices synced properly had
mis-aligned SDP pins. This patch fixes the math to calculate the correct
seconds alignment for the PPS signal.

Signed-off-by: Jacob Keller <jacob.e.keller@intel.com>
Tested-by: Phil Schmitt <phillip.j.schmitt@intel.com>
Signed-off-by: Jeff Kirsher <jeffrey.t.kirsher@intel.com>