Just found this useful and wanted to share it in case it helps others.
If you are missing installed apps from the MY Apps section of the market then delete the market update on the phone and go back into the market.
Settings/Applications/Manage Applications/Market - Unistall Update
Then go back to the market app and accept the agreement.
Hopefully all your apps should be listed again under My Apps.
I spent ages trying to fix this and this method worked perfectly for me so hopefully it might be useful.
If you are missing installed apps from the MY Apps section of the market then delete the market update on the phone and go back into the market.
Settings/Applications/Manage Applications/Market - Unistall Update
Then go back to the market app and accept the agreement.
Hopefully all your apps should be listed again under My Apps.
I spent ages trying to fix this and this method worked perfectly for me so hopefully it might be useful.