If you edit an instrument in GarageBand 2 and save it using the same name as the original, only the edited version of the instrument will appear when you set Jam Pack Management to Show All.
To avoid this issue, always save any edited version of an instrument with a new name. This way, both the original and the edited version will be available to use.
In GarageBand 3.0.2 or later, it is no longer possible to save an instrument with the same name as one of the default instruments. If you attempt to do so, you will be prompted to use a different name.