It depends on when you upgraded.
To clarify
You install applications
We release version with the admin CP marketplace
You upgrade. It asks you at that point to match them to their marketplace items
I suspect that last part is what hasnt happened. We can match them up for you if you let us know what they are, but as mentioned, you should check with the authors first of all. If you want us to go ahead regardless, let us know, but it may break things if there is a good reason for them being custom