If I put a chart on the same sheet as the data it references its cell references are updated as I insert/delete rows on the sheet. If I put the same chart on a different worksheet (or use a chart sheet) the references aren't updated. The insertrows and deleterows calls have true specified for the updatereference parameter and non-chart references on the sheets are updating correctly.
Could you create a simple test code with the template file, zip it and post us here to reproduce the issue you have talked about, we will check it soon.