Hi all, thank you very much for all the help you offered! :)
It works now! Robert Nelson, who maintains the kernel for the Beagleboard Black gave me the hint to try the kernel version 3.18.rc7 (mainline), which receives a lot of upgrades concerning AT91 systems, which the Arietta G25 is one of. Additonally from the Acmesystems mailing list I got the hint to explicetly set the clock frequencies of the XTALs in the dts file. After mixing everything together, recompiling the kernel and installing it on the board I now have a Gentoo system with the correct time (which was way off after a short period with previous kernel versions) and 'shutdown -h -H now' now correctly powers down the board. I am happy! :) Best regards, Meino