Copying my response to ubuntu-users:

One of the peculiarities of this stuff (FlexNet and others) is that
uninstalling the proprietary software in question doesn't necessarily
actually remove all its remnants from the machine; from what we can
tell, this appears to be deliberate, in order to enforce things like
trial periods even across uninstall/install cycles.

http://www.chiark.greenend.org.uk/~cjwatson/blog/windows-applications-making-grub2-unbootable.html
 may be of some help in understanding the background; that was part of my 
attempt to gather information in order to put in place what eventually
turned into the warning message you're seeing.

Note that this is *not* an error message; it is a warning.  An error would mean 
that there is some problem that couldn't be fixed
automatically.  But in this case, it's only a warning: GRUB is telling you that 
it worked around a problem.  You can ignore this message if you like.

The reason GRUB reports this message, even though inevitably not everyone will 
understand it or be able to do much with it (remember it's only written to the 
terminal, so it's not very intrusive) is that we have no other way to encourage 
people to complain to the vendors of the proprietary software in question that 
abuses bits of the boot area.  Their misbehaviour can have much more serious 
consequences if there is already a boot loader in place there when the 
proprietary software tries to write its licence tracking stuff there; GRUB 
actually has to implement error correction in assembly on its own boot code in 
order to
stop this rendering systems unbootable, which is a non-trivial maintenance 
cost!  We therefore need some kind of way to exert pressure on these vendors, 
even if it's small and indirect.

We can't really give much more information in the warning message,
because that would involve us putting in a lot of time researching the
quirks of proprietary software rather than developing free software.
The current situation seems like a reasonable compromise, because at
least we don't silently brush the problem under the carpet.

I hope that this message will turn up for future people searching for
this problem.

** Changed in: grub2 (Ubuntu)
       Status: New => Won't Fix

** Changed in: grub2 (Ubuntu)
     Assignee: (unassigned) => Colin Watson (cjwatson)

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https://bugs.launchpad.net/bugs/1560130

Title:
  Grub reports conflict in sector usage.

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