The type mis-match was due to an error when the data was imported from text file to the ALIR worksheet. an '=' was prepended to certain data that started with a '-'.
I amended the error catch code to help find this.
The issue I have now is the length of time taken for the code to execute.
With 10,000 rows in the CUCM worksheet being compared to 400,000 rows in the ALIR worksheet to find matches office is being locked up while the code executes not just excel. Excel shows 'not responding' in the window title bar.

Does anyone have an idea as to how i can made the coding run quicker?

the following code shows my modifications to help catch this data error.
Sub Button1_Click()
Dim LastALIRRow As Long
Dim LastResultRow As Long
Dim DestinationRow As Long
Dim ALIRSourceRow As Long
Dim CUCMSourceRow As Long
Dim MainLoop As Long
Dim MatchType As Integer

On Error GoTo Errorcatch

'Get Last Row containing Data on ALIR Worksheet (Could be up to 400,000 rows)
LastALIRRow = ALIR.UsedRange.Rows.Count
'Initialise Variables before loop
DestinationRow = 3
ALIRSourceRow = 2
CUCMSourceRow = 2
MatchType = 5
MainLoop = 2
'Get Last Row containing Data on Results Worksheet
LastResultRow = Results.UsedRange.Rows.Count
'Clear Cells of Data on Results Worksheet
Results.Range(Cells(3, 1), Cells(LastResultRow, 9)).ClearContents
'Apply NOFill to Cells on Results Worksheet
Results.Range(Cells(3, 1), Cells(LastResultRow, 9)).Interior.ColorIndex = 0

Do While CUCM.Cells(CUCMSourceRow, 3).Value < ""
Do While MatchType = 5 And MainLoop < LastALIRRow + 1
'Check if match for First and Last name and User ID
If UCase(CUCM.Cells(CUCMSourceRow, 4).Value) = UCase(ALIR.Cells(MainLoop, 15).Value) And UCase(CUCM.Cells(CUCMSourceRow, 2).Value) = UCase(ALIR.Cells(MainLoop, 14).Value) And (UCase(CUCM.Cells(CUCMSourceRow, 1).Value) = UCase(ALIR.Cells(MainLoop, 11).Value) Or UCase(CUCM.Cells(CUCMSourceRow, 1).Value) = UCase(ALIR.Cells(MainLoop, 12).Value)) Then
'Check if match for Phone Number
If CUCM.Cells(CUCMSourceRow, 5).Value = Right(ALIR.Cells(MainLoop, 34).Value, 10) Then
MatchType = 1
ALIRSourceRow = MainLoop
Else
MatchType = 2
ALIRSourceRow = MainLoop
End If
Else
'Check if match for Phone Number
If CUCM.Cells(CUCMSourceRow, 5).Value = Right(ALIR.Cells(MainLoop, 34).Value, 10) Then
MatchType = 3
ALIRSourceRow = MainLoop
End If
End If
MainLoop = MainLoop + 1
Loop
If MatchType < 5 Then
Call WriteRow(ALIRSourceRow, CUCMSourceRow, DestinationRow, MatchType)
DestinationRow = DestinationRow + 1
End If
CUCMSourceRow = CUCMSourceRow + 1
MatchType = 5
MainLoop = 2
Loop
CUCM.Cells(3, 11).T
Exit Sub

Errorcatch:
MsgBox Err.Description
MsgBox "CUCM Row " & CUCMSourceRow
MsgBox "ALIR Row " & ALIRSourceRow
MsgBox "Match Type " & MatchType
MsgBox "Loop Counter " & MainLoop


End Sub



Function WriteRow(ByVal ALIRSourceRow As Long, _
ByVal CUCMSourceRow As Long, _
ByVal DestinationRow As Long, _
ByVal MatchType As Integer)
Dim ALIRSourceCol(1 To 2) As Integer
Dim CUCMSourceCol(1 To 5) As Integer
Dim LoopCount As Integer
Dim GREEN As Integer
Dim YELLOW As Integer
Dim ORANGE As Integer
Dim BLUE As Integer

ALIRSourceCol(1) = 21 'Principal Country Location
ALIRSourceCol(2) = 28 'Unique Key
CUCMSourceCol(1) = 1 'First Name
CUCMSourceCol(2) = 2 'Last Name
CUCMSourceCol(3) = 3 'User ID
CUCMSourceCol(4) = 4 'Department


GREEN = 43
YELLOW = 6
ORANGE = 45
BLUE = 23


For LoopCount = 1 To 4
CUCM.Cells(CUCMSourceRow, CUCMSourceCol(LoopCount)).Copy
Results.Cells(DestinationRow, LoopCount).PasteSpecial (xlPasteValues)
Application.CutCopyMode = False
Next LoopCount

For LoopCount = 1 To 2
ALIR.Cells(ALIRSourceRow, ALIRSourceCol(LoopCount)).Copy
Results.Cells(DestinationRow, (LoopCount + 4)).PasteSpecial (xlPasteValues)
Application.CutCopyMode = False
Next LoopCount

Results.Cells(DestinationRow, 7).Value = MatchType
Results.Cells(DestinationRow, 8).Value = CUCMSourceRow
Results.Cells(DestinationRow, 9).Value = ALIRSourceRow

Select Case MatchType
Case 0
Case 1
For LoopCount = 1 To 7
Results.Cells(DestinationRow, LoopCount).Interior.ColorIndex = GREEN
Next LoopCount
Case 2
For LoopCount = 1 To 7
Results.Cells(DestinationRow, LoopCount).Interior.ColorIndex = YELLOW
Next LoopCount
Case 3
For LoopCount = 1 To 7
Results.Cells(DestinationRow, LoopCount).Interior.ColorIndex = ORANGE
Next LoopCount
Case 4
For LoopCount = 1 To 7
Results.Cells(DestinationRow, LoopCount).Interior.ColorIndex = BLUE
Next LoopCount
End Select
End Function