Either I cannot reproduce it, or it works different in the version I am using ( 1.3 DailyBuild Aug 17 2015 ), or maybe there is some misunderstanding here.
What I did:
1. Create camera, add render elements.
2. Press render - VFB pops up, image is rendering, press and hold on "save" button, select "save all"
3. Beauty + all elements get saved as test1_XXX.jpg
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4. Change camera position, etc
5. Press render - VFB pops up, image is rendering, press and hold on "save" button, select "save all"
6. Beauty + all elements get saved as test2_XXX.jpg
So I get 2 different versions of beauty + elements as expected.
On the other hand, if you press "save" only (not "save all"), then only the beauty pass will get saved, without all the other elements. Maybe this is what you did?