a url still opens in old version of firefox after new version is installed

I realize my timing of testing Ubuntu may have been consequential in finding this bug. (There is a time when a new version of something is released, but it's not pushed through the update system yet.) But even if you install an Internet Explorer update before it's pushed to Windows Update, it still works well and easily as the default browser.

Could you be more specific about the version of Ubuntu and firefox where you had this problem.

I'm guessing you tried to install Firefox 3.5 in Ubuntu 9.04. This is not allowed . Since Ubuntu 9.04 supports firefox 3.0 and not 3.5
There are strict policies of which update land in Stable releases.

Not allowing it is the annoyance. I can understand not pushing through the Ubuntu update system, but what reason could there be for not allowing it to be updated?

Even if you have a reason, it wouldn't out-weigh the annoyance factor.

Thank you for bringing this bug to our attention. However, a paper cut should be a small usability issue, in the default Ubuntu 9.10 install, that affects many people and is quick and easy to fix. So this bug can't be addressed as part of this project.

- This was never a problem in karmic nor will this likely be a problem in stable releases, Which will usually be having the latest versions. And changing the update policy is not a papercut issue.
For further information about papercuts criteria, please read https://wiki.ubuntu.com/PaperCut.

This is done to maintain the stability of the release and not to expose the stable releases to any unknown bugs.
You mention IE updates in windows , but you also need to remember that with every update there were several users who said that the IE update broke the web pages or there were other problems. There were even several mentions on the web to not install the immediate update of the IE8 as there were problems. this has negative impact on the stability of the OS.
 This policy is to maintain that none of these problems arise in Ubuntu.
But, I agree that when an user explicitly selects the new version the preferred app also can be changed , the you could bring up such discussion in the desktop mailing list > https://lists.ubuntu.com/mailman/listinfo/ubuntu-desktop
You can read more about the update policy > https://wiki.ubuntu.com/StableReleaseUpdates

To prevent your problem where the uri opens with firefox 3 , you can change the default web browser to firefox 3.5 [or shiretoko]from the System > Preferences> Preferred applications menu.