To recreate:
1) Add 4 terms in a vocabulary (say tags) at admin/structure/taxonomy/tags viz, a,b,c,d
2) Reshuffle the terms by drag and drop to have the order b,d,c,a and "Save"
3) Now on the terms page hit "Reset to Alphabetical". Drupal asks for a confirmation. Hit "Reset to Alphabetical" on the confirmation page. The changes are saved and you are now sent back to your page showing list of terms.
4) Ideally all your settings are now saved and you are on terms list page. Hitting Save button again on this page should not have any effect. Now hit "Save" button on the terms list page.
What Happens: The terms reorder themselves as they were before we did "Reset to Alphabetical"
Expected Behaviour: The terms should still remain in the "Alphabetically Reset Order"
Courtesy: The issue was actually reported by Mr Chetan from Intel Bangalore (India)