Usually if the master bullets don't apply to the layouts it means that someone at some time has manually modified the layouts. Sadly there is no simple way to reverse this unless you are ably to modify the XML code to unset the manual bullets or remake all of the layouts. Both are going to be quite a job!
You might be able to automate remaking the layouts with code. Make sure you try this on a copy as it isn't foolproof!
Copy the code below and in PPT Alt f11 to get to the code editor. INSERT > Module and paste in the code f5 to run it. If you are lucky it might fix thinks in seconds.
Code:
Sub fixPLC()
Dim ocl As CustomLayout
Dim oshp As Shape
Dim sngL As Single
Dim sngT As Single
Dim sngW As Single
Dim sngH As Single
Dim P As Long
Dim raySize(7) As Long
For Each ocl In ActivePresentation.SlideMaster.CustomLayouts
For Each oshp In ocl.Shapes
If oshp.Type = msoPlaceholder Then
If oshp.PlaceholderFormat.Type = 7 Then
sngW = oshp.Width
sngH = oshp.Height
sngT = oshp.Top
sngL = oshp.Left
For P = 1 To oshp.TextFrame2.TextRange.Paragraphs.Count
raySize(P) = oshp.TextFrame2.TextRange.Paragraphs(P).Font.Size
Next P
oshp.Delete
With ocl.Shapes.AddPlaceholder(7)
.Width = sngW
.Left = sngL
.Top = sngT
.Height = sngH
For P = 1 To .TextFrame2.TextRange.Paragraphs.Count
.TextFrame2.TextRange.Paragraphs(P).Font.Size = raySize(P)
Next P
End With
End If
End If
Next oshp
Next ocl
End Sub