From you command that you use, I see no problem at all.
I would say that the -S is optional, and if you want to update all segments, then you don't need it.
Now... I would suggest to try to install the latest fix pack for V9, which is at the time of writing FP5. And try again. If that doesn't work, then something is fishy!!!
Would it be possible to share how the AG and APP are done? Maybe we can help that way.