I can confirm this problem. I have a lacie external hard drive with a
few partitions. It has an apple partition map and boot sector on it
along with some ext partitions (one for gentoo and one for file storage)

The problem looks like a permissions problem that happens when the drive
automounts. The folder that the ext partitions mount to, "/media/disk"
has root as the owner. If I plug in a regular vfat usb stick it mounts
with the correct permissions (User is owner) and it can be
unmounted/ejected with no problems.  It can easily be corrected with a
chown on the directory, but who really wants to do that?

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nautilus cannot unmount USB media containing multiple partitions
https://bugs.launchpad.net/bugs/108643
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