I cannot reproduce the issue.
On my machine the focus shifts nicely to the new window every time.

Hmmm, in that case it looks like Elive has a script or setting tucked away that overrides it.

I don't have any issues with all the stuff I have launched through "startup-applications.list" entries like: diodon, syncthing, blueman-applet, nm-applet, notifications, gxkb and disk-indicator.

Solved. :)
Issue is gone in git version 653a456a02 release 0.24.1

The pager in the bar starts "shaking" the moment you create multiple horizontal rows of VirtualDesktops.
I suspect it's a size issue too i.e they wont fit within the constraints of the ibar size setting.

There is another point in:
If you create a new shelf and solely add the pager to that it will set itself better than as to desktop or as a desktop overlay.
Resizing the pager to a larger up to maximum size makes it flicker (but not with all sizes) i.e renders it useless.

Confirmed!!
Works fine now.

Sorry, that was a size issue ......... the buttons under the screen did not show up on my screen.
Without "magnification" of the screen they show up.

Yeah, I'm not surprised but it doesn't get a beauty prize for that and in fact makes enabling EFM less desirable.

Running 0.23.99.0 on Elive-3.8.2 amd64 Beta on multiple machines.
Sorry about that.

Sorry, I forgot.
That's Enlightenment 0.23.99.0 on Elive 3.8.2 amd 64 beta......on multiple machines.