YES!!!! I've come across this exact scenario, and found it a bit frustrating / bewildering. So I considered the following:
1. Add ?:refresh=yes onto the workbook that points at this published datasource. Did not go down this path, because it essentially nullifies cache altogether, and I only wanted to invalidate cache upon refresh of the tde
2. Change the caching options to balanced. Did not go down this path, because it changes the caching server wide, and I was interested in doing this just for this intra-day data refresh workbook
* 3. Went with this option. Embedded the extract within the workbook instead of using a published datasource. Then when refreshing the extract, the fresh data comes through, perhaps the old cache is invalidated, and it works!!!!