Not sure if others are still searching for a solution to this problem. Some of our users were also experiencing this issue and was found not to be caused by any Add-in issues.
We tried the following workaround for the problem and it has resolved the issue for our users. Would be interested to see if it also solves the problems for others...
The work around basically replaced the standard Excel close behaviour by a controlled close within the Workbook_BeforeClose event
Private Sub Workbook_BeforeClose(Cancel As Boolean)
Dim intResponse As Integer
'If the workbook needs to be saved then ask the user if they want to save the workbook, if not then exit without saving
'Need a global boolean to ensure the request to save the workbook is not shown twice
If Not ThisWorkbook.Saved And Not blnStartedClose Then
blnStartedClose = True
intResponse = MsgBox("Do you want to Save the this Workbook" & vbNewLine & vbNewLine & _
"Select 'Yes' to save the workbook" & vbNewLine & _
"Select 'No' to close without saving", vbYesNo, "Confirm - Workbook Save?")
If intResponse = vbYes Then ThisWorkbook.Save
'If the user has clicked on 'No' to save the workbook then reset the "Saved" property to TRUE so that when we exit this routine no attempt to save the workbook is made
ThisWorkbook.Saved = True