The fix will be available in the R1 2018 SP2 Release.

It happens when the Pane is dragged and dropped not on the Compass several times, quickly.

Available in LIB version 2017.3.1225, it will be also available in the R1 2018 Release.

The compasses of the other ToolWindow appear.

workaround:
add the following visual state to the DocumentHostTemplate of the RadPaneGroup:

<VisualStateManager.VisualStateGroups>
    <VisualStateGroup x:Name="DropDownDisplayStates">
        <VisualState x:Name="DropDownButtonCollapsed" />
        <VisualState x:Name="DropDownButtonVisible">
            <Storyboard>
                <ObjectAnimationUsingKeyFrames Storyboard.TargetName="DropDownButtonElement" Storyboard.TargetProperty="Visibility">
                    <DiscreteObjectKeyFrame KeyTime="0">
                        <DiscreteObjectKeyFrame.Value>
                            <Visibility>Visible</Visibility>
                        </DiscreteObjectKeyFrame.Value>
                    </DiscreteObjectKeyFrame>
                </ObjectAnimationUsingKeyFrames>
            </Storyboard>
        </VisualState>
    </VisualStateGroup>
</VisualStateManager.VisualStateGroups>

and remove the trigger targeting the drop down button.

Available in LIB version: 2017.2.605

Available in LIB version 2017.1.410 , it will be also available in the R2 2017 Release. 

The the keyboard focus is also lost if you undock a RadPane from its docked state.
As a workaround you can persist the focus as shown in the RestoreFocusOnStateChanged SDK example, that can be found here:
https://github.com/telerik/xaml-sdk/tree/master/Docking/RestoreFocusOnStateChanged

When the control contains RadPane instances which Content is provided by a MAF framework that content experiences flickers and disappearing when the RadPane is being floated, docked, pinned or unpinned.

On Deferred mode, you can still undock panes (for example, but context menu).
The problem starts when you want to dock them back, When moving a pane above the compass, it hides the compass (And this problem is a PITA when you docking with the inner compass (rather than the root compass), since the left,top, center etc.. arrows are near to each other (so you are not 100% sure you hit the right arrow).

This happens in particular scenario after saving/loading the layout.

With three split containers in one other and no document host resizing between the first and second containers causes the first and third containers to resize, instead of the first and second containers.

1. Create an app using RadDocking. The 'First Look' demo of RadDock can be modified to reproduce the problem.
2. Modify one of the panes, replace the TextBlock control with a TextBox control. Bind the text of the TextBox control to a string property.
3. Add the string property to the .cs file and in the setter, Show a MessageBox.
4. Run app. Select tab with Textbox control and modify the value.
5. Now select the other tab. the messagebox will be displayed. Notice it can be dismissed via keyboard but not via mouse click. It cannot be moved via mouse either.
6. Select a window outside of the application and not select the message box. Notice Mouse input now works. MessageBox can be moved and dismissed via mouse.

If the IsContentPreserved of a PaneGroup is SET to true and a RadTabControl is placed inside a Pane the focus is moved through its content.