If I understand correctly, you've configured the Flatrate module to calculate a per-product rate, but for one or more of the products in your cart you've edited the product page to override that store default rate with a product-specific rate? And on the checkout page you see the correct calculation (using the product-specific rates)? You select that shipping option and move to the next page, the order review page, where you see a different dollar amount listed for shipping?

I can't reproduce that. But one thing I did find out while testing is that uninstalling the old Flatrate doesn't seem to remove the Workflow-ng configurations for the old module. You need to go into admin/build/workflow-ng to edit the old Flatrate configurations and deactivate them. You will recognize the old configurations because they will be named something like "Flat rate per product" and "Flat rate per order", whereas the new Flatrate you set up at admin/store/settings/quotes/methods/flatrate will have a descriptive name of your own choosing.

Note also that you have to run update.php with the new Flatrate module enabled! If you ran update.php before enabling the new version of the module, then it didn't update the Flatrate tables. You can run it again in your current configuration without harming anything. (I don't think this is the problem, because you are getting quotes...).

This doesn't sound like a PHP version problem, since you're now actually getting quotes and not seeing error messages. I'm using PHP 5.2.3.