Used ironically. Both verb and noun have changed in the course of this proverb's history, the earliest instance of the present form thus far discovered being quot. 1898. Jump used absolutely in the sense of ‘agree completely’ or ‘coincide’ is now archaic.
Though he made that verse, Those words were made before. ‥Good wits doe iumpe.
[1618 D. Belchier Hans Beer-Pot D1]
Great wits jump: for the moment Dr. Slop cast his eyes upon his bag‥the very same thought occurred.
[1761 Sterne Tristram Shandy III. ix.]
As great minds jump this proves‥that my Mind is Great!
[1889 A. James Journal 1 Dec. (1964) 61]
Curious how great minds think alike. My pupil wrote me the same explanation about his non-appearance. ‥
[1898 C. G. Robertson Voces Academicae 24]
‘Great minds think alike—that's why we're never in agreement.’
[2002 Washington Times 28 May C9 (Bottomliners cartoon)]
Related to: coincidence; harmony and disharmony
Bibliography of major proverb collections and works cited from modern editions is available here.
