Hi Gabe,
I have used SGP 2.5.1.17 with a slightly older PHD2 (phd2-2.6.1dev11 but I have not yet tried 2.6.2) with my A-P1100GTO and never once had a Meridian Flip issue. Every single SGP Sequence with Meridian Flip enabled, it has worked perfectly. The only difference is I don't have APCC.
Peter (AKA Peter in Reno from CN)