Here's a demonstration of how a VBA UDF can change the colouring of a sheets contents rather than using conditional formatting.
As long as both sheets have rows and columns sorted in the same order then this will compare for differences in every cell between two seperate Excel sheets.
You can add this into as many cells as you need to on a third sheet to detect differences between the same two cells on the two sheets with data on: =DifferenceTest(Sheet1!A1,Sheet2!A1)
And the function to be stored in the VBA editor as follows:
Function DifferenceTest(str1 As String, str2 As String) As String
If str1 = str2 Then
Application.Caller.Font.ColorIndex = 2
Else
Application.Caller.Font.ColorIndex = 3
DifferenceTest = str1 & " vs " & str2
End If
End Function