Hi bouke I am a not GNU parted maintainer, but I am a both a Debian Developper and Atari 16/32 bits user so I can help digging the Atari specific problems here.
Could you please share the sfdisk sda-pt.sf you used to create the partition table or the MBR of the disk having the problem ? There is also one tool available in the debian archive, disktype, which also knows both the Atari ST partitioning scheme, AHDI and MSDOS. It would be interesting to see what disktypes output in your case ( and which logic it uses for the detection)
