Comparison Macro - excel

Question

I have a macro that does the following:
SETUP:
Compares a ID# between the "April Count" and "Prg-Srv Data" and turns the ones that are in common to a green cell background.
Filters the common data (anything with a green cell background) and copies that to a new worksheet "Medicaid Report". Then clears the AutoFilter and and formats the worksheet to specified style.
Filters and removes any rows that contain the word "Duplicate".
Finally it compares the April Count to the Medicaid Report to see if anyone has been missed from the April Count list.
PROBLEM IS THIS:
When the macro is finished it is still "randomly" marking data in the April Count that is also in the Medicaid Report and I'm not sure what I have done wrong.
Also if there is a more efficient way to do this let me know, this macro takes a long time to run and I'm not sure if its just because it has to do 5,000+ records or if I coded inefficiently. Thanks
CODE:
Sub ComparePrgSrv()
'Get the last row
Dim Report As Worksheet
Dim Report2 As Worksheet
Dim Report3 As Worksheet
Dim i, j, k As Integer
Dim LastRow, LastRow2, LastRow3 As Integer
Dim UniqueVal As New Collection
Dim Val As String
Set Report = Excel.Worksheets("April Count")
Set Report2 = Excel.Worksheets("Prg-Srv Data")
Set Report3 = Excel.Worksheets("Medicaid Report")
LastRow = Report.UsedRange.Rows.count
LastRow2 = Report2.UsedRange.Rows.count
LastRow3 = Report3.UsedRange.Rows.count
Application.ScreenUpdating = False
'April Count to Program Services comparison.
For i = 2 To LastRow2
For j = 2 To LastRow
If Report2.Cells(i, 1).Value <> "" Then 'This will omit blank cells at the end (in the event that the column lengths are not equal.
If InStr(1, Report.Cells(j, 1).Value, Report2.Cells(i, 1).Value, vbTextCompare) > 0 Then
Report2.Cells(i, 1).Interior.Color = RGB(0, 102, 51) 'Dark green background
Report2.Cells(i, 1).Font.Color = RGB(0, 204, 102) 'Light green font color
Exit For
Else
Report2.Cells(i, 1).Interior.Color = xlNone 'Transparent background
Report2.Cells(i, 1).Font.Color = RGB(0, 0, 0) 'Black font color
End If
End If
Next j
Next i
'Filter Program Services to show correct data.
Report2.Range("$A$1:$M$" & LastRow2).AutoFilter Field:=1, Criteria1:=RGB(0, 102, 51), Operator:=xlFilterCellColor
'Copy filtered data to new worksheet.
Report2.Range("$A$1:$M$" & LastRow2).SpecialCells(xlCellTypeVisible).Copy Destination:=Worksheets("Medicaid Report").Range("A1")
'Clear filter selection on both sheets.
Report.AutoFilterMode = False
Report2.AutoFilterMode = False
'Format cell colors on Medicaid sheet.
Report3.UsedRange.Interior.Color = xlNone 'Transparent background
Report3.UsedRange.Font.Color = RGB(0, 0, 0) 'Black font color
Report3.Range("$A$1:$M$1").Interior.Color = RGB(31, 73, 125) 'Blue background
Report3.Range("$A$1:$M$1").Font.Color = RGB(255, 255, 255) 'White font color
'Filter and Delete Rows Containing "DUPLICATE"
With ActiveSheet
.AutoFilterMode = False
With Range("B1", Range("B" & Rows.count).End(xlUp))
.AutoFilter 1, "*DUPLICATE*"
On Error Resume Next
.Offset(1).SpecialCells(12).EntireRow.Delete
End With
.AutoFilterMode = False
End With
'April Count to Medicaid Report comparison.
For i = 2 To LastRow
For j = 2 To LastRow3
If Report.Cells(i, 1).Value <> "" Then 'This will omit blank cells at the end (in the event that the column lengths are not equal.
If InStr(1, Report3.Cells(j, 1).Value, Report.Cells(i, 1).Value, vbTextCompare) > 0 Then
Report.Cells(i, 1).Interior.Color = xlNone 'Transparent background
Report.Cells(i, 1).Font.Color = RGB(0, 0, 0) 'Black font color
Exit For
Else
Report.Cells(i, 1).Interior.Color = RGB(156, 0, 6) 'Dark red background
Report.Cells(i, 1).Font.Color = RGB(255, 199, 206) 'Light red font color
End If
End If
Next j
Next i
End Sub
Workbook Setup:

Answer 1

First off, what do you mean by
"When the macro is finished "
For the effectiveness part:
You should remove the If Report2.Cells(i, 1).Value <> "" Then as it is already taken in account with the InStr. If cell is empty InStr will evaluate as 0; that should speed up a bit.
Secondly, you should get the last row of data using this:
LastRow = Report.Range("a" & Report.Rows.Count).End(xlUp).Row
LastRow2 = Report2.Range("a" & Report2.Rows.Count).End(xlUp).Row
LastRow3 = Report3.Range("a" & Report3.Rows.Count).End(xlUp).Row
"a" being the column containing the data to be checked. This will give you exactly the last non-empty row of the aimed column instead of the total used range of the entire sheet.
Also, in VBA, when you declare variables on one line, this:
Dim i, j, k As Integer
will only declare "k" as an Integer but "i" and "j" will be Variant
You should write it as:
Dim i As Integer, j As Integer, k As Integer. Same remark for Dim LastRow, LastRow2, LastRow3 As Integer
And don't forget to enable the Application.ScreenUpdating before exiting the Sub.