I'm not sure if this helps, but I've encountered the "Partition 2 does not end 
on a cylinder boundary." message before. Thus on another distribution, and not 
on a ThinkPad, and with another partition with its own bootloader that didn't 
want to boot up after grub. Anyway. Are you able to mount the diagnostic 
partition? Because in my experience I could mount the partition that didn't 
want to boot. And when I removed the newly created partition with parted, 
things started to happen again.
But as I said. This might be a complete different case, but I'm thinking about 
a bad partition table that might be corrected if the partition in question is 
removed.

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after installing Ubuntu I can't access my rescue partition
https://bugs.launchpad.net/bugs/19634
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