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I'm running Ubuntu 16.04 LTS host with VirtualBox 5.1.38 from Oracle's repository.

I have Ubuntu 18.04.1 LTS guest on this host.
Inside the guest I have installed all needed packages to get Guest Additions (GA) installed successfully - build-essential, dkms, linux-headers-generic.
Then I insert VBoxGuestAdditions_5.1.38.iso to virtual VM drive and successfully installed it with its autorun prompt.
Then after reboot I see that all GA functionality work as expected, so I have all necessary processes:

$ uname -r
4.15.0-32-generic

$ sudo ps ax | grep -i vbox
  442 ?        I<     0:00 [iprt-VBoxWQueue]
  822 ?        Sl     0:00 /usr/sbin/VBoxService --pidfile /var/run/vboxadd-service.sh
 1393 ?        S      0:00 /usr/bin/VBoxClient --clipboard
 1394 ?        Sl     0:00 /usr/bin/VBoxClient --clipboard
 1398 ?        S      0:00 /usr/bin/VBoxClient --checkhostversion
 1399 ?        S      0:00 /usr/bin/VBoxClient --checkhostversion
 1404 ?        S      0:00 /usr/bin/VBoxClient --display
 1405 ?        S      0:00 /usr/bin/VBoxClient --display
 1412 ?        S      0:00 /usr/bin/VBoxClient --seamless
 1413 ?        Sl     0:00 /usr/bin/VBoxClient --seamless
 1420 ?        S      0:00 /usr/bin/VBoxClient --draganddrop
 1421 ?        Sl     0:00 /usr/bin/VBoxClient --draganddrop

But after next kernel upgrade (as simple as sudo apt update && sudo apt dist-upgrade) I get the following logs

$ cat /var/log/syslog | grep -i vboxadd
Jan  9 12:01:45 bionic vboxadd.sh: Building the VirtualBox Guest Additions kernel modules.
Jan  9 12:01:45 bionic vboxadd.sh: Building the main Guest Additions module.
Jan  9 12:02:17 bionic vboxadd.sh: .
Jan  9 12:02:17 bionic vboxadd.sh: Building the shared folder support module.
Jan  9 12:02:24 bionic vboxadd.sh: .
Jan  9 12:02:24 bionic vboxadd.sh: Building the graphics driver module.
Jan  9 12:02:32 bionic vboxadd.sh: .
Jan  9 12:02:32 bionic vboxadd.sh: Doing non-kernel setup of the Guest Additions.

and after reboot I see that clipboard and dragandrop are switched off:

$ uname -r
4.15.0-43-generic

$ sudo ps ax | grep -i vbox
  428 ?        I<     0:00 [iprt-VBoxWQueue]
 1404 ?        S      0:00 /usr/bin/VBoxClient --checkhostversion
 1405 ?        S      0:00 /usr/bin/VBoxClient --checkhostversion
 1409 ?        S      0:00 /usr/bin/VBoxClient --display
 1410 ?        S      0:00 /usr/bin/VBoxClient --display
 1419 ?        S      0:00 /usr/bin/VBoxClient --seamless
 1912 ?        S      0:00 /usr/bin/VBoxClient --seamless

Why does this happen? How to avoid GA re-installation from iso file?

I understand that this problem may be a bit complex, but Ubuntu newbies may expect that it works on VirtualBox without issues, so please do not close this question as off-topic. Kernel updates are released very often so it may become a bit annoying.

1

Try to remove Guest Additions, installed using the ISO file provided by the host with

sudo /opt/VBoxGuestAdditions-5.1.38/uninstall.sh

and then install the following deb-packages directly available in your guest Ubuntu

sudo apt install virtualbox-guest-x11 virtualbox-guest-utils

This should give you the same features than installing manually the guest addition.

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