I have an app that processes Word, PowerPoint and Excel documents. After processing each document, I call the SaveAs method (or SaveAs2). For word, I set the DisplayAlerts to wdAlertsAll. I never see the dialog asking if I want to overwrite the document. I added code to get the alsert level right before calling SaveAs2 and it is wdAlertsAll. But, I see no message box. If I run Word and open the same file and do SaveAs to the same location as my app, the dialog appears.
I have the same issue with PowerPoint where I set the level to ppAlertsAll.
I do the same thing for Excel and ... it works just fine. I am prompted before doing the SaveAs.
In all three cases my app starts the Office apps and make sure they are visible on the desktop. I was thinking that perhaps running in the background was an issue but apparently not.