I assume you're waiting long enough for System Picker to find the System Folders -- it can take several minutes...

Anyway, you can "bless" the new System Folder manually:

1) Open the desired System Folder on a window.

2) Take the System file out from it -- for instance, drag it on the desktop.

3) Close the window.

4) Open the System Folder again.

5) Drag the System file back into the open window -- the subfolders inside (Apple Menu Items, Extensions, Control Panels, etc) should get their usual custom icons at once.

6) Close the window and you're done! The closed System Folder should have the Mac icon, indicating that it's blessed.

In case the custom icons don't appear at step 5, maybe you'll have to "unbless" (or at least make unblessable) the currently active System Folder:

1) Open the current System Folder on a window.

2) Take the System file out from it, but do not drag it on the same place you'll drop the other System File! For instance, make a new folder ('old system') on the desktop for it.

3) Repeat the previous directions for the System Folder you want to bless.

Once you see the custom icons, that folder is blessed

Hope this helps,