Found the reason for the problem and a workaround.

The problem:

The problem is having a RAID partition as the last partition of the device. 
Because the superblock location of a partition that is the last on the device 
and the superblock location of an entire device is the same (both on the end of 
the device) the superblock metadata should be used to find which RAID device 
it's related to.
Apparently grub-probe misunderstands this info. In my case it was assuming I 
had a full hard drive RAID device instead of a single partition at the end.

The workaround:

Having found this erratic behavior, I changed my disk partition layout so that 
the RAID partition wouldn't be at the end of the disk. Now, the last partition 
was the swap partition.
That change itself didn't work because the mkswap command didn't erase the raid 
superblock data still in the partition at the end of the drive. I had to do a 
"mdadm --zero-superblock" at the disk device so that the only valid superblock 
would be the RAID partition superblock.

After all this, I finally got grub-probe to detect my configuration
successfully.

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https://bugs.launchpad.net/bugs/816475

Title:
  package grub-pc 1.99~rc1-13ubuntu3 failed to install/upgrade:
  ErrorMessage: subprocess installed post-installation script returned
  error exit status 139

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