There is an extra step that you need to take when upgrading from one edition of SQL Server 2008 to another, for example when upgrading from Express to Express with Tools. This extra step is called Edition Upgrade (sometimes SKU Upgrade) and the net result is that you have to run the install wizard twice when upgrading an existing instance to a different edition.
Why did we do it?
I don't have all the technical details here (I'm not a setup guy) but the basic deal is that the feature tree you see when installing is based on information about the edition that has already be put on the machine. When you're upgrading from one edition to another, the information on the machine is about the old edition, so you have to first update that information to specify the new edition before you can add new features related to the new edition.
In general Edition Upgrade is a rare occurance, but it happens more often for Express users since it's likely that you've installed some other product such as Visual Studio, that included only the core Express edition and you want to add a feature from one of the more complete editions such as Express with Tools.
What do we do?
Edition Upgrade is really just another trip through the install wizard in which you provide the Product Key for the new edition. When you're moving to a paid edition, this would involve actually typing the new Product Key that was provided with your new edition, but since all Express editions have pre-populated Product Keys, this new step is really just a matter of downloading the package for the new edition (I suggest you save it to your Hard Drive since you'll need to run it twice) and running through it twice.
The first time you run the package you'll need to select the option to upgrade to a different edition. This will run through a set of checks and give you the option to provide the new Product Key, or in the case of Express product you'll see the page where the new Product Key is supplied for you, you don't type it in yourself. Once you've completed the Edition Upgrade, you run the install wizard again, this time choosing the option to Add Features to an existing Instance. Several more wizard pages and you'll get to the feature tree that will have all the features available in the new instances listed.
There's always an exception, what is it?
Yes, there's always an exception. In this case the exception is that we were able to elimnate the Edition Upgrade step between SQL Express with Tools and SQL Express with Advanced Services. If you already have SQL Express with Tools installed and you'd like to add a feature from Express Advanced (say Full Text Search) you can go directly to Add Feature option and skip the Edition Upgrade.
Hopefully this helps clarify things when you're upgrading your edition.