Yes, tr, you are correctly understanding the problem.

I took the following steps with bazaar build 733 and workflow_ng 1.6:

1. Deactivate the flatrate shipping method in shipping quotes.
2. Deselect the uc_flatrate module from the modules page.
3. Verify that the flatrate method had disappeared from Workflow_ng. It had, I did not need to remove it manually.
4. Uninstall the flatrate module.
5. Re-activate the flatrate module from the modules page.
6. Check the database via update.php. No updates needed. Ran it anyway.
7. Verify that workflow_ng didn't have a flatrate shipping method.
8. Set up a new flatrate method with my store defaults for flatrate shipping.
9. Verify that workflow_ng still didn't have a flatrate shipping method.
10. Activate the flatrate shipping method in store/configuration
11. Verify that the new shipping method was indeed listed in workflow_ng.
12. Checked a random product--one that hadn't been used for a trial purchase to be sure no cache problem. Verified the product shipping rate is $20.00. Default store rate is $25.00 with $5.00 handling.
13. Cleared the browser cache so no confusion about any previous pages or purchases.
14. Tested with a trial purchase of the product I checked in step 12.
15. When I enter my address on the checkout page, the shipping charge is correctly shown as $25.00. When I advance to the to the review checkout page, the shipping charge is shown as $30.00--the default store rate.

Still a problem!

I do have a reputation for being able to easily break code. I have at times done a lot of beta testing. My favorite was the time I was testing a product near the end of the testing cycle. They were confident in error free code (yeah, right!) and had offered a bounty of $200 per reproducible bug. I was able to find 26 reproducible problems within an hour or so of testing. I stopped because I wasn't sure they pay up. Wish I could do that more often...

Something is broken here. It could be something in my configuration, but I can't see any configs that could be broken. Or something in the code. I am willing to continue checking my configs--or to test new code.