Solution if anybody else might find this useful:
The issue was even though column 1 was entered as a Column Reference H for example the COUNTIF function required this as a numeric reference so added an extra variable on the column1 value to the numeric value and modified the formula to suit. All working now:
Dim LastRow As Long
Dim column1 As String
'display an input box asking for column
column1 = InputBox( _
"Please enter column to ckeck")
'if no file name chosen, say so and stop
ColumnNumber = Columns(column1).Column
' MsgBox ColumnNumber
If Len(column1) = 0 Then
MsgBox "No column entered"
Exit Sub
End If
Dim column2 As String
'display an input box asking for column
column2 = InputBox( _
"Please enter column to insert results")
'if no file name chosen, say so and stop
If Len(column2) = 0 Then
MsgBox "No column entered"
Exit Sub
End If
'-------------------------------------------------------
'This is the original version of my script with set columns which works great.....
'LastRow = Range("B" & Rows.Count).End(xlUp).Row
' With Range("E1")
' .FormulaR1C1 = "=COUNTIF(C2,RC[-3])"
' .AutoFill Destination:=Range("E1:E" & LastRow)
' Range("E1").Select
' ActiveCell.FormulaR1C1 = "Duplicates"
'-----------------------------------------------------
LastRow = Range(column1 & Rows.Count).End(xlUp).Row
With Range(column2 & "1")
.FormulaR1C1 = "=COUNTIF(C" & ColumnNumber & ",C" & ColumnNumber & ")"
.AutoFill Destination:=Range(column2 & "1" & ":" & column2 & LastRow)
Range(column2 & "1").Select
ActiveCell.FormulaR1C1 = "Duplicates"
End With
End Sub