That alert has nothing to do with the comparison, really. It's telling you the document has a corrupt table. You should fix that. Instead of using 'Open and Repair' as the dialogue suggests, corrupt tables can often be 'repaired' by converting the tables to text and back again or by saving the document in RTF format, closing the document then re-opening it and re-saving in the doc(x) format – or see the macro below.
Code:
Sub TableRepair()
'Macro to repair damaged tables by saving each table in an RTF-format file, then
' reinserting the table from the RTF-format file into the source document.
Application.ScreenUpdating = False
Dim Rng As Range, i As Long, RTFDoc As Document, strPath As String
With ActiveDocument
strPath = .Path & "\"
For i = .Tables.Count To 1 Step -1
Set Rng = .Tables(i).Range
Set RTFDoc = Documents.Add(Visible:=False)
With RTFDoc
.Range.FormattedText = Rng.FormattedText
.SaveAs2 FileName:="strPath & RTFDoc.RTF", Fileformat:=wdFormatRTF, AddToRecentFiles:=False
.Close
End With
Set RTFDoc = Documents.Open(FileName:="strPath & RTFDoc.RTF", AddToRecentFiles:=False, Visible:=False)
Rng.Tables(1).Delete
With RTFDoc
Rng.FormattedText = .Tables(1).Range.FormattedText
.Close
End With
Kill "strPath & RTFDoc.RTF"
Next
End With
Set Rng = Nothing: Set RTFDoc = Nothing
Application.ScreenUpdating = True
End Sub