Hello.
I have the same problem on both ubuntu 16.04 and 18.10.
The problem appeared after removing a logical partition from and extended.

* The extended partition is correctly displayed in gnome-disk-utility after 
system start up
* The extended partition does not show anymore in gnome-disk-utility after 
gparted is launched (until next startup).
* The extended partition does not show anymore in gnome-disk-utility after 
creating then removing a new logical partition in gnome-disk-utility (until 
next startup).
* The extended partition is correctly displayed in gparted.

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https://bugs.launchpad.net/bugs/1641308

Title:
  Partitions display wrong in gnome -disks - ok in gparted

Status in gnome-disk-utility package in Ubuntu:
  Confirmed

Bug description:
  The partitions displayed by gnome-disk-utility are wrong. When i use
  gparted the partitions displayed are correct.

  The display became wrong after i deleted 1 partition from the disk
  using gnome-disk-utility.

  Here is a screenshot of the 2 tools vision of the same disk:
  http://pasteboard.co/PjWpqeNzi.png

  Here is the fdisk:
  hippo@hippo-camp:~$ sudo fdisk -l
  [sudo] password for hippo: 
  Disk /dev/sdc: 465,8 GiB, 500107862016 bytes, 976773168 sectors
  Units: sectors of 1 * 512 = 512 bytes
  Sector size (logical/physical): 512 bytes / 512 bytes
  I/O size (minimum/optimal): 512 bytes / 512 bytes
  Disklabel type: dos
  Disk identifier: 0x1c0966b0

  Device     Boot     Start       End   Sectors   Size Id Type
  /dev/sdc1  *           63 758587953 758587891 361,7G  7 HPFS/NTFS/exFAT
  /dev/sdc3       758589438 903041023 144451586  68,9G  5 Extended
  /dev/sdc5       758589440 903041023 144451584  68,9G 83 Linux

  
  hippo@hippo-camp:~$ lsb_release -rd
  Description:  Ubuntu 16.04.1 LTS
  Release:      16.04

  gnome-disk-utility:
    Installed: 3.18.3.1-1ubuntu1
    Candidate: 3.18.3.1-1ubuntu1
    Version table:
   *** 3.18.3.1-1ubuntu1 500
          500 http://archive.ubuntu.com/ubuntu xenial/main amd64 Packages
          100 /var/lib/dpkg/status

  gparted:
    Installed: 0.25.0-1
    Candidate: 0.25.0-1
    Version table:
   *** 0.25.0-1 500
          500 http://archive.ubuntu.com/ubuntu xenial/main amd64 Packages
          100 /var/lib/dpkg/status

  I get *very nervous* when tools that have write access to partitions
  can't display them properly.

  
  Good hunt
  Matt

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: gnome-disk-utility 3.18.3.1-1ubuntu1
  ProcVersionSignature: Ubuntu 4.4.0-47.68-generic 4.4.24
  Uname: Linux 4.4.0-47-generic x86_64
  NonfreeKernelModules: nvidia_uvm nvidia_drm nvidia_modeset nvidia
  ApportVersion: 2.20.1-0ubuntu2.1
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Sat Nov 12 12:16:39 2016
  ExecutablePath: /usr/bin/gnome-disks
  InstallationDate: Installed on 2016-10-11 (31 days ago)
  InstallationMedia: Ubuntu 16.04.1 LTS "Xenial Xerus" - Release amd64 
(20160719)
  SourcePackage: gnome-disk-utility
  UpgradeStatus: No upgrade log present (probably fresh install)

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