My first thought was that your "comments" may have in fact been other objects designed to behave in a similar way
BUT - by transferring everything to a new file you have disproved that thought 
Default comment settings apear here:
File \ Option \ Advanced - Comment options appear in Display category
BUT - this must be correctly set already - otherwise all workbooks would display the same symptoms
The VBA to toggle those settings:
With Application
If .DisplayCommentIndicator = xlNoIndicator Then
.DisplayCommentIndicator = xlCommentIndicatorOnly
Else
.DisplayCommentIndicator = xlNoIndicator
End If
End With
BUT - again this would set the global variable and would apply to all workbooks
One way to mimic the symptoms:
Private Sub Workbook_Open()
Application.DisplayCommentIndicator = xlNoIndicator
End Sub
Private Sub Workbook_BeforeClose(Cancel As Boolean)
Application.DisplayCommentIndicator = xlCommentIndicatorOnly
End Sub
That would leave other workbooks unaffected (unless open at the same time)
Hover characteristics are not something we have much control over, so there is a possibility that your workbook could be corrupted in some way
- in which case all you can do is to create a new file and move all your data and VBA.
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