Arggggggg!
Here are a couple of macros that may help accomplish the task or at least find out what the deal is.
To put them into A COPY OF ONE OF THE WORKBOOKS for trial, follow the instructions on this page:
http://www.contextures.com/xlvba01.html#Regular
Try the FindInteriorColorCode() routine first: select one of those shaded cells and run it and see what value it returns. -4142 means it doesn't think it's shaded at all.
Now, if that returns a positive value, then try running the second routine, PlaceXinShadedCells(), while one of the shaded cells is still selected. See if that works worth a darn. And if it doesn't, at least you haven't lost anything since you should be
using a copy of the workbook (or make a copy and try all of this in the original).
Sub FindInteriorColorCode()
'choose a cell and then run this code
'from [View] {Macros}
MsgBox "Cell " & ActiveCell.Address & " interior Color Index is " _
& ActiveCell.Interior.ColorIndex
'-4142 is no shading/color
'3 is standard red
'Excel 2010 dark red is 18
End Sub
Sub PlaceXinShadedCells()
Dim myColorIndex As Integer
Dim anyCell As Range
'select one "sample" cell before running this macro
myColorIndex = ActiveCell.Interior.ColorIndex
For Each anyCell In ActiveSheet.UsedRange
If anyCell.Interior.ColorIndex = myColorIndex Then
'only place x in cell if it is empty
If IsEmpty(anyCell) Then
anyCell.Value = "x"
End If
End If
Next
MsgBox "Task completed"
End Sub