VBA Conditional Formatting Issue

I am having issues setting conditional formatting via VBA. I am setting it this was since when the code deletes my rows the formatting is deleted as well. The problem I have is, it does not properly set the formatting. It should be setting at follows but it mixing the two together in a sense.

Border:

• If A5 is not blank it should add cell borders through T to the bottom of the entire workbook.

Gray Fill:

• If A5 is not blank it should fill column Q & R to the bottom of the entire workbook.

It is difficult to provide a sample workbook, but if required I will do my best to get a mock up.

My current code is as follows:

Option Explicit

Public Sub LoadEffort()

'//||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\\'
'||   Open all Excel files in a specific folder and combines data into one sheet                               ||'
'||   John_w (10/8/2010 )     (2007-2010 compatible)                                                           ||'
'||   http://www.mrexcel.com/forum/excel-questions/500421-macro-merge-multiple-files-into-one-worksheet.html   ||'
'\\||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||//'

    Dim path As String
    Dim shtDest As Worksheet
    Dim Wkb As Workbook
    Dim CopyRng As Range, Dest As Range
    Dim RowofCopySheet As Integer
    Dim selectedFiles As Variant, filename As Variant
    Dim i As Long
    Dim LR As Long
    Dim rngFilter As Range
    Dim r As Long, f As Long
    Dim GetDesktop As String
            
    Application.ScreenUpdating = False
    Application.Calculation = xlManual
        
'// Deletes the Effort Dump sheet data to prepare for new report being imported.\\'

        Sheets("Effort Dump").Activate
        Set rngFilter = ActiveSheet.AutoFilter.Range
        r = rngFilter.Rows.Count
        f = rngFilter.SpecialCells(xlCellTypeVisible).Count
        If r > f Then
        ActiveWorkbook.Worksheets("Effort Dump").AutoFilter.Sort.SortFields.Clear
        ActiveSheet.ShowAllData
        End If
        i = Range("A" & Rows.Count).End(xlUp).Row + 3
        If i = 4 Then
            Range("A5").Select
        Else
            Rows("5:5").Select
            Range(Selection, Selection.End(xlDown)).Select
            Range(Selection, Selection.End(xlDown)).Select
            Selection.Delete
            With Sheet11
                With Sheet11.Range("A:T")
                    .FormatConditions.Delete
                End With
                With .Range("$A$5:$T$1048576")
                    .Activate
                    .FormatConditions.Add xlExpression, Formula1:="=NOT(ISBLANK($A5))"
                    .FormatConditions(1).Borders.LineStyle = xlContinuous
                    .FormatConditions(1).Borders.Weight = xlThin
                End With
                With .Range("$Q$5:$R$1048576")
                    .Activate
                    .FormatConditions.Add xlExpression, Formula1:="=NOT(ISBLANK($A5))"
                    .FormatConditions(1).Interior.ColorIndex = 48
                End With
            End With
            Range("A5").Select
        End If
        Set shtDest = ActiveWorkbook.Sheets("Effort Dump")

'// Importing of the new files.\\'
                
    RowofCopySheet = 2 ' Row to start on in the sheets you are copying from
    GetDesktop = CreateObject("WScript.Shell").SpecialFolders("Desktop") & _
        Application.PathSeparator

    path = GetDesktop
    
    selectedFiles = SelectFiles(path)

    If IsArray(selectedFiles) Then
    
        Application.EnableEvents = False
        
'// Open and merge each selected file
        
        For Each filename In selectedFiles
            If filename <> ActiveWorkbook.FullName Then
                Set Wkb = Workbooks.Open(filename)
                With Wkb.Sheets(1)
                    Set CopyRng = .Range(.Cells(RowofCopySheet, 1), _
                        .Cells(Cells(Rows.Count, 1).End(xlUp).Row, .Cells(1, Columns.Count).End(xlToLeft).Column))
                End With
                Set Dest = shtDest.Range("A" & shtDest.UsedRange.SpecialCells(xlCellTypeLastCell).Row + 1)
                CopyRng.Copy
                Dest.PasteSpecial xlPasteValuesAndNumberFormats
                Application.CutCopyMode = False 'Clear Clipboard
                Wkb.Close False
            End If
        Next
    
        Application.EnableEvents = True

    Range("A1").Select
    
    MsgBox "Processing Complete."
    
    Else
    
        MsgBox "No files were selected"
    
    End If
    
    Application.ScreenUpdating = True
    
    Application.Calculation = xlAutomatic
    
End Sub

Private Function SelectFiles(startFolderPath As String) As Variant

    Dim Filter As String
    Dim FilterIndex As Integer
    
    'File filters
    Filter = "Excel workbooks (*.xls), *.xls"
    FilterIndex = 1
    
    'Set start drive and path
    ChDrive (startFolderPath)
    ChDir (startFolderPath)
    
    With Application
        'Get array of selected file(s)
        SelectFiles = .GetOpenFilename(Filter, FilterIndex, "Select File(s) to Merge", , MultiSelect:=True)
        
        'Reset start drive and path
        ChDrive (.DefaultFilePath)
        ChDir (.DefaultFilePath)
    End With

End Function

EDIT: I am using Excel 2013.