I have not heard of a problem of StampAll missing some documents that are in the collection, so you might want to call Lotus Support with a simple case that demonstrates the problem. However, if you have to iterate through the documents anyway, it’s much more efficient to do all your assignments at that time, and not use StampAll at all.
One thing you might watch out for, is that the NotesView object’s AutoUpdate property should be set to False. If you don’t do this, the contents of your collection might change out from under you. I can’t tell whether this has anything to do with your problem, but if you’re making changes that would affect the order or membership of documents in the view, then iterating through the collection might well be chancy — even for StampAll.