If the colors did not change chances are they didn't follow the master correctly in the first place.
Some simple code might help
Make one shape how you want it and SELECT it.
Alt f11 to open the code editor
Insert >> Module
Copy and past in this code
Code:
Sub fixMe()
Dim oshp As Shape
Dim osld As Slide
ActiveWindow.Selection.ShapeRange(1).PickUp
For Each osld In ActivePresentation.Slides
For Each oshp In osld.Shapes
If oshp.Type = msoAutoShape Then oshp.Apply
Next oshp
Next osld
End Sub
Using a copy just in case it's not what you want f5 to run or View > Macros > Run