If there's a security issue the macro won't run at all next time Outlook is opened, so the fact that it does suggests this is not the issue.
Sometimes For Each ... Next loops don't behave well so try
Public Sub SaveAttachmentsToDisk(Item As Outlook.MailItem)
Dim Atmt As Attachment
Dim FileName As String
Dim myExt As String
Dim lngIndex As Long
For lngIndex = 1 To Item.Attachments.Count
Set Atmt = Item.Attachments(lngIndex)
myExt = Mid(Atmt.FileName, InStrRev(Atmt.FileName, Chr(46)))
Select Case myExt
Case ".pdf"
FileName = "\\AP Invoices for Processing" & _
Format(Item.CreationTime, "yyyymmdd_hhmmss_") & Atmt.FileName
Atmt.SaveAsFile FileName
Case Else
End Select
Next lngIndex
lbl_Exit:
Set Atmt = Nothing
Exit Sub
End Sub