1265 MHz is indeed wrong and that is what causes your timing/clock issues. There have been some Sam460 boards which use a different onboard reference clock, namely 50Mhz instead of 55Mhz. The 3.9 boot.img assumes a 55MHz clock which causes the off by factor 1.1 result.
Thanks for your answer. One question though: is this fixed in morphos 3.10 :) ?
Edit: Acube has a nice utility to check the reference clock (checkbaseclock). It's included with the new version of uboot. I just executed this utility again, and indeed it says my sam has a 50 Mhz. clock.[ Edited by Mozzerfan 10.11.2016 - 22:31 ]