Be double-sure that you went into the old Messaging application > Settings > and uncheck "Notifications". Maybe even a reboot on your phone to clear out the notification coming from the original messenger app.
It sounds to me like it is still sending you notifications if you click on unread messages in the notifications pull-down and it is taking you to old messaging app.
As for the unread messages always showing on the lock screen, this is along the same lines as many others are experiencing (including me). It has been posted in many different ways, but no one has an answer as of yet.
It comes down to the fact that even though you have changed it so that the default SMS messaging application will not notify you that there was a new message (thereby eliminating double-notifications), it still thinks that there is a new message until you open the default SMS messaging application and view the messages.
This happens with any 3rd party messaging application, including
GoSMS,
chompSMS and
Handcent.
For example, if I wanted to get rid of the "1 message" notification on the lock screen. If I get a SMS text message, go to Handcent and view the message. I must then close Handcent and go to the old Messaging application and view the message again.
Not familiar with the Droid apps, but seems like the 3rd party application should be able to make a call to the OS that the SMS message was read.
Anyway, wish I had the answer for you, but just hope the smart folks here get it figured out for us...
