Interesting. I'll give a try based on the ancient saves I found here and will let you know.
EDIT : Done. It appears that starting from v.25.0, you only find the Staff of Wisdom if you are at the right point of Ivy's progress.
Here's what I tried: starting from a save from 20.1 (before the "Mortimer's book" quest point of Ivy's progress), I explored Melkor's Realm with versions 25.2-EX, 25.2-DUNGEON, 25.0 and 24.2d. Except for the latter, the Staff of Wisdom was nowhere to be found (it was there when entering level 27 on v24.2d though). Then I progressed the story up to the point of Ivy's progress where she finds about Soran's safeguard and asks you to find another plan. After that I went back to Melkor's Realm and found the Staff when entering level 27, on all versions after 24.2d.
Question is: Are you sure that you are at the right point of Ivy's story to rightfully expect the Staff to be there? If yes, then you are facing a bug (I can propose a workaround though: download version 24.2d, load your save, speedrun to level 27, grab the Staff and exit, save, and then get back to version 25.2). If not, well, you know what you have to do.