My VM is @ 1280 x 1024.
@lolwhites, 1920x1080 is very close to my 1920x1200 with problems. Unfortunately, I wouldnāt think it a good workaround to set lesser.
@gabdub, 1280x1024 compares to my VM with little issue at 1680x1050.
I do know one thing. VirtualBox guesses and retains monitor resolution settings of the guest and I donāt know of any way to force it. Changing resolutions takes a few reboots to train it back to a lower resolution and it does not store in snapshots. You actually end up fighting with Ubuntuās automatic resolution setting.
Something in the panel code is miscalculating or similar. It could be related to HiDpi changes. More testing this weekend - I really need something for bug reporting. 
EDIT: Anyone else with 1920x1080, 1920x1200 or similar seeing saved panel layout issues?
My native deskotp PC is 1366x768.
My VM was pretty close(something like 1366x6**).\
I currently donāt have any UM VM installed, I had to delete it after I messed it up intentionally; 
Iām pretty busy now with my exam and thesis workā¦ Iāll install again sometime later and experiment some more!
Something else has cropped up that may or may not be related.
I noticed that there was no Caja shortcut in the launcher, so I added one manually. I then noticed Iād acquired a second set of panel applets and global menu.
Furthermore, I just launched Firefox to make this post but the icon does not appear in the launcher. The other shortcuts I added manually are still present.
Coincidence?
Time hasnāt been on my side but I did try a few things. Iām concentrating almost entirely on being able to save and restore panel layouts which is by far my easiest way to create this issue.
Making a VM 1920x1200 does bring out this problem. This is complicated by how VirtualBox stores monitor size and reports it back to the VM separately (not part of a snapshot).
Changing a problematic 1920x1200 system (native install) to low res, like 1280x1024, does NOT fix the issue. However, the hardware continues to report the monitor is 1920x1200 (no physical monitor change).
re:
org/mate/panel/general/object-id-list
org/mate/panel/objects
No doubt about this - the duplicates often appear in āobjectsā but does not actually appear in a panel if not present in āobject-id-listā. Once these two places are out of sync the fun (saving or rebooting) starts.
When duplicates appear they are often a different name like this:
ORIGINAL DUPLICATED AS
========================= =========================
object-3 launcher (MATE-Tweak)
notification-area notificationarea
object-0 mateweatherapplet
clock clockapplet Netbook name
object-4 shutdown
show-desktop showdesktopapplet Redmond name
window-list windowlistapplet
workspace-switcher workspaceswitcherapplet
A developer intimately familiar with how this works may instantly be able to pinpoint the code but creating a reproducible set of steps is elusive past ākeep trying, itāll do itā.
Using mate tweak and restoring my saved panel configuration ended up in double applets as you mention. Also when I tried to switch panels with the tweak tool I had strange behavior like double panels sitting on top of each other, panels not loading at all etc. My solution is not to use mate tweak for any thing panel related.
Hi @django, Yep, sounds exactly like my system. As discussed above, it seems worse on 1920x1200 and 1920x1080 resolutions. Howās that compare?
i donāt think itās related to screen resolution. 1366 768 here.