Sem saber exatamente o que pretende, a unica situação que chama atenção e que a variável col01, somente recebe um valor se checkbox15 for true, porem a mesma é utilizada em quase todos os demais if's

Private Sub CommandButton1_Click()
Dim col01 As Range, col02 As Range, col04 As Range, col06 As Range
Dim col07 As Range, col08 As Range, col09 As Range
Dim col031 As Range, col032 As Range, col033 As Range, col034 As Range
Dim col051 As Range, col052 As Range, col053 As Range, col054 As Range
Dim Rng As Range, Intervalo As Range

Dim PrimeiraOcorrencia As String
Dim mVetor As Variant
Dim Contador As Long
Dim I As Long
Dim NovaPlanilha As Worksheet

If CheckBox6.Value = True Then
    CheckBox7.Value = True
    CheckBox8.Value = True
    CheckBox9.Value = True
    CheckBox10.Value = True
    CheckBox11.Value = True
    CheckBox12.Value = True
    CheckBox13.Value = True
    CheckBox14.Value = True
Else
    If CheckBox7.Value = True Then
        AFRE = "AFRE"
    Else
        AFRE = ""
    End If
    
    If CheckBox8.Value = True Then
        GEFAZ = "GEFAZ"
    Else
        GEFAZ = ""
    End If

    If CheckBox9.Value = True Then
        TFAZ = "TFAZ"
    Else
        TFAZ = ""
    End If
    
    If CheckBox10.Value = True Then
        AFAZ = "AFAZ"
    Else
        AFAZ = ""
    End If

    If CheckBox11.Value = True Then
        AUSG = "AUSG"
    Else
        AUSG = ""
    End If

    If CheckBox12.Value = True Then
        OSO = "OSO"
    Else
        OSO = ""
    End If

    If CheckBox13.Value = True Then
        EPPGG = "EPPGG"
    Else
        EPPGG = ""
    End If
    
    If CheckBox14.Value = True Then
        OUTRAS = "OUTRAS"
    Else
        OUTRAS = ""
    End If
End If

If Trim(AFRE) <> "" Then
    mVetor = Array("AFRE")
    Set NovaPlanilha = Worksheets.Add
    Contador = NovaPlanilha.Range("A1048576").End(xlUp).Row
    Sheets("REMUNERACAO BASICA").Select
    
    With Worksheets("REMUNERACAO BASICA").Range("a1:C5000")
        For I = LBound(mVetor) To UBound(mVetor)
            Set Intervalo = .Find(What:=mVetor(I), After:=.Cells(.Cells.Count), LookAt:=xlPart, _
                            SearchOrder:=xlByRows, SearchDirection:=xlNext, MatchCase:=False)
            If Not Intervalo Is Nothing Then
                PrimeiraOcorrencia = Intervalo.Address
                Intervalo.Copy NovaPlanilha.Range("C" & Contador)
    
                If CheckBox15.Value = True Then
                    'MASP
                    Set col01 = Intervalo.Offset(0, -2)
                    col01.Copy NovaPlanilha.Range("A" & Contador)
                ElseIf CheckBox40.Value = True Then
                    'NOME
                    Set col02 = Intervalo.Offset(0, -1)
                    col02.Copy NovaPlanilha.Range("B" & Contador)
                ElseIf CheckBox42.Value = True Then
                    'SÍMBOLO
                    Set col031 = Application.Worksheetfuntion.VLookup(col01, Worksheets("CARGOS DAD").Range("B2:C171"), 2, False)
                    col031.Copy NovaPlanilha.Range("C" & Contador)
                    Set col032 = Application.Worksheetfuntion.VLookup(col01, Worksheets("CARGOS FGD").Range("B2:C69"), 2, False)
                    col032.Copy NovaPlanilha.Range("D" & Contador)
                    Set col033 = Application.Worksheetfuntion.VLookup(col01, Worksheets("CARGOS GTED").Range("B2:C35"), 2, False)
                    col033.Copy NovaPlanilha.Range("E" & Contador)
                    Set col034 = Application.Worksheetfuntion.VLookup(col01, Worksheets("CARGOS 6762").Range("B2:E780"), 4, False)
                    col034.Copy NovaPlanilha.Range("F" & Contador)
                ElseIf CheckBox18.Value = True Then
                    'EXERCÍCIO
                    Set col04 = Application.Worksheetfuntion.VLookup(col01, Worksheets("R:Arquivo ProcessosAtos-AtualOUTROSTRABALHO CCBASE DE DADOSRELATÓRIO CARGOS").Range("A1:AY4012"), 51, False)
                    col04.Copy NovaPlanilha.Range("G" & Contador)
                ElseIf CheckBox48.Value = True Then
                    'VALOR CC
                    Set col051 = Application.Worksheetfuntion.VLookup(col01, Worksheets("CARGOS DAD").Range("B2:C171"), 13, False)
                    col051.Copy NovaPlanilha.Range("H" & Contador)
                    Set col052 = Application.Worksheetfuntion.VLookup(col01, Worksheets("CARGOS FGD").Range("B2:C69"), 13, False)
                    col052.Copy NovaPlanilha.Range("I" & Contador)
                    Set col053 = Application.Worksheetfuntion.VLookup(col01, Worksheets("CARGOS GTED").Range("B2:C35"), 12, False)
                    col053.Copy NovaPlanilha.Range("J" & Contador)
                    Set col054 = Application.Worksheetfuntion.VLookup(col01, Worksheets("CARGOS 6762").Range("B2:E780"), 12, False)
                    col054.Copy NovaPlanilha.Range("K" & Contador)
                ElseIf CheckBox52.Value = True Then
                    'REMUNERACAO S/CC
                    Set col06 = Intervalo.Offset(0, 66)
                    col06.Copy NovaPlanilha.Range("L" & Contador)
                ElseIf CheckBox56.Value = True Then
                    'REMUNERACAO C/CC
                    Set col07 = Application.Worksheetfuntion.VLookup(col01, Worksheets("REMUNERACAO COM CARGO").Range("A3:B9000"), 2, False)
                    col07.Copy NovaPlanilha.Range("M" & Contador)
                ElseIf CheckBox21.Value = True Then
                    'DIFERENCA S/CC C/CC
                    Set col08 = col07.Value - col06.Value
                    col08.Copy NovaPlanilha.Range("N" & Contador)
                ElseIf CheckBox45.Value = True Then
                    '% DIFERENCA SOBRE REMUNERACAO
                    Set col09 = (col08.Value / col06.Value) * 100
                    col09.Copy NovaPlanilha.Range("O" & Contador)
                End If
            Do
                Contador = Contador + 1
                Set Intervalo = .FindNext(Intervalo)
                Loop While Not Intervalo Is Nothing And Intervalo.Address <> PrimeiraOcorrencia
            End If
        Next I
    End With
End If
End Sub