Sounds like your control ordering is wrong if you're having an issue with the menu strip. The designer will insert controls into the form in the order you added them to the designer. In some cases if the ordering is wrong then you get issues with docking overwriting other controls. It sort of sounds like your menu strip was perhaps added after the other controls which causes it to overlay them incorrectly. Adjusting the order in the designer.cs should resolve that.
Example.
Public Class Form1
Private Sub NewToolStripMenuItem_Click(sender As Object, e As EventArgs) Handles NewToolStripMenuItem.Click
_count += 1
Dim id = _count
Dim title = $"MDI {id}"
Dim form = New Form()
form.BackColor = Color.Yellow
form.Text = title
form.MdiParent = Me
form.WindowState = FormWindowState.Maximized
Dim label = New Label
label.Text = title
form.Controls.Add(label)
form.Show()
End Sub
Private Shared _count = 0
' Auto generated by VS
Private Sub InitializeComponent()
Me.MenuStrip1 = New System.Windows.Forms.MenuStrip()
Me.NewToolStripMenuItem = New System.Windows.Forms.ToolStripMenuItem()
Me.MenuStrip1.SuspendLayout()
Me.SuspendLayout()
'
'MenuStrip1
'
Me.MenuStrip1.Items.AddRange(New System.Windows.Forms.ToolStripItem() {Me.NewToolStripMenuItem})
Me.MenuStrip1.Location = New System.Drawing.Point(0, 0)
Me.MenuStrip1.Name = "MenuStrip1"
Me.MenuStrip1.Size = New System.Drawing.Size(800, 24)
Me.MenuStrip1.TabIndex = 1
Me.MenuStrip1.Text = "MenuStrip1"
'
'NewToolStripMenuItem
'
Me.NewToolStripMenuItem.Name = "NewToolStripMenuItem"
Me.NewToolStripMenuItem.Size = New System.Drawing.Size(43, 20)
Me.NewToolStripMenuItem.Text = "&New"
'
'Form1
'
Me.AutoScaleDimensions = New System.Drawing.SizeF(6.0!, 13.0!)
Me.AutoScaleMode = System.Windows.Forms.AutoScaleMode.Font
Me.ClientSize = New System.Drawing.Size(800, 450)
Me.Controls.Add(Me.MenuStrip1)
Me.IsMdiContainer = True
Me.MainMenuStrip = Me.MenuStrip1
Me.Name = "Form1"
Me.Text = "Form1"
Me.MenuStrip1.ResumeLayout(False)
Me.MenuStrip1.PerformLayout()
Me.ResumeLayout(False)
Me.PerformLayout()
End Sub
End Class
Each child window is maximized in the parent. The menu does not overlay them as there is a label at the 0,0 position and it is shown properly. Since the children are maximized closing a child window will have the previous child maximized as well.