vba - Conditional Formatting Excel document via VB6 (issue with overwriting formats)

I'm creating an Excel document at runtime that has a bunch of values I'd like to have conditionally formatted. In going through various attempts from scratch as well as using/modifying code outputted from the Excel's macro recorder, I'm having a consistent issue related to formatting overwrites.

I've posted a snippet of the code below and can say that I've tested to ensure my selection ranges are valid and appropriate for what I want conditionally formatted. There is some overlap but what's bizarre is that the first conditional format takes on just one property of the second conditional format. Meaning D5:End of the worksheet ends up having a green color font as opposed to the red it should be. Commenting each section of the code does allow them to work independently but I'm guessing this is an issue with specifying conditional formats further somehow? I've tried a few different case scenarios and below is the code with modifications:

EDIT (Updated Code):

'First conditional format, check sheet for values > 50 and make text red.
With xl.range("D5:" & theLastColumn & lastRow)
  .FormatConditions.add Type:=xlCellValue, Operator:=xlGreater, Formula1:="=50"
  With .FormatConditions(1).Font
    .Color = -16383844
    .TintAndShade = 0
  End With
  .FormatConditions(1).StopIfTrue = False
End With


'Second conditional format, check specific row (row 5 in the example) 
'for values > 40, and fill interior with green in addition to dark green text.
With xl.range("D" & Infectivity & ":" & theLastColumn & Infectivity)
  .FormatConditions.add Type:=xlCellValue, Operator:=xlGreater, Formula1:="=40"
  With .FormatConditions(2).Font
    .Color = -16752384
    .TintAndShade = 0
  End With
  With .FormatConditions(2).Interior
    .PatternColorIndex = xlAutomatic
    .Color = 13561798
    .TintAndShade = 0
  End With
End With

So what's the best way to have multiple conditional formats (that may overlap ranges) and still have them all function as intended? I've tried debugging this so much I'm certain there's something easy I'm overlooking. I've also tried a few different methods to specify separate formatconditions(1) and formatconditions(2) but still receive strange issues.

EDIT:

VBA Code where I continue to have the same issue.

Sub conditionalFormat()
  With Range("D5:BA9")
    .FormatConditions.Add Type:=xlCellValue, Operator:=xlGreater, Formula1:="=50"
    .FormatConditions(.FormatConditions.Count).SetFirstPriority
    With .FormatConditions(1).Font
      .Color = -16383844
      .TintAndShade = 0
    End With
    .FormatConditions(1).StopIfTrue = False
  End With

  With Range("D9:BA9")
    .FormatConditions.Add Type:=xlCellValue, Operator:=xlGreater, Formula1:="=40"
    With .FormatConditions(2).Font
      .Color = -16752384
      .TintAndShade = 0
    End With
    With .FormatConditions(2).Interior
      .PatternColorIndex = xlAutomatic
      .Color = 13561798
      .TintAndShade = 0
    End With
    .FormatConditions(2).StopIfTrue = False
  End With    
End Sub

Even with the SetFirstPriority on the appropriate (red text) conditional format, it just gets overwritten somehow. Am I missing something here?

Answer

After much thought and reworking the code we came to the conclusion that what I was doing (multiple conditions overlapping) was the cause of the mixed results. At the simplest level, I was able to add .FormatConditions.Delete to my additional conditional formats to ensure only one format was applied.

The corrected final code is shown below:

Dim Infectivity As Long
Infectivity = Application.WorksheetFunction.match("Infectivity", range("A1:" & "A" & lastRow), 0)

With xl.range("D5:" & theLastColumn & lastRow)
    .FormatConditions.add Type:=xlCellValue, Operator:=xlGreater, _
    Formula1:="=50"
    .FormatConditions(.FormatConditions.count).SetFirstPriority
With .FormatConditions(1).Font
    .Color = -16383844
    .TintAndShade = 0
End With

    .FormatConditions(1).StopIfTrue = False
End With

If Infectivity > 0 Then
With xl.range("D" & Infectivity & ":" & theLastColumn & Infectivity)
    .FormatConditions.Delete
    .FormatConditions.add Type:=xlCellValue, Operator:=xlGreater, _
     Formula1:="=40"
With .FormatConditions(1).Font
    .Color = -16752384
    .TintAndShade = 0
End With
With .FormatConditions(1).Interior
    .PatternColorIndex = xlAutomatic
    .Color = 13561798
    .TintAndShade = 0
End With
.FormatConditions(1).StopIfTrue = False
End With
End If

My downfall was related to the macro recorder giving me a false of the ideal method of formatting these cells. It's always best to simplify before moving forward.

Major thanks to Siddharth Rout for all the help.