I seem to have seen similar behavior in Excel before. Certain things (query tables in Excel and charts in PowerPoint) don't seem to refresh as long as VBA is executing. In Excel, if your code closes the workbook with the query tables that are supposed to update, it will interrupt your code and ask if you want to cancel the pending refresh.
For this specific problem PowerPoint, when VBA closes the workbook that is the source of the data for the chart, PowerPoint doesn't update the chart. I'm having to leave the workbooks open and have the user close them all.
I've seen suggested workarounds for this type of thing such as Application.EnableEvents=True or inserting a Wait, but I've never gotten them to work and PowerPoint doesn't seem to have an equivalent for EnableEvents anyway.
I'm sure someone's run into this? Is there a workaround that won't have me leaving things open for the user to close them?