Specific reasons were not released. A statement was released, but it was substantially discredited. The best I can figure, is that the balance of the members of the Holy Synod and the "First among them," could not get along, they were not of one mind about administrative issues. My sense is that Metropolitan Jonah was inexperienced and did not know how to work cooperatively with the the balance of the Synod, the officers of the OCA at the Chancery in Syosset (Oyster Bay Cove), and the Metropolitan Council. You'll recall he attempted to fire Fr. Alexander Garclavs, the Chancellor, but the Synod had engaged him and they reluctantly honored Met. Jonah's request, and Fr. Alexander is a well respected cleric, a fine clergyman, and Met. Jonah's inability to work with him is more of a reflection on Met. Jonah, than a criticism of Fr. Alex. After a meeting of the Lesser Synod in early July, 2012, the new Chancellor, Fr. John Jillions, went to Washington, and on behalf of the Holy Synod, asked Met. Jonah to draft a letter of resignation, which he did. (There are all sorts of stories about political differences, which I do not believe.) No one made any allegations of any canonical infractions. I think Met. Jonah had difficulty working within the conciliar organs and statutes of the OCA, which limit the canonical authority of a bishop and a primatial hierarch. My feeling is, as a former Abbot of a monastery with essentially unilateral authority, Met. Jonah just didn't seem to come to terms with the environment in which an OCA Primate must function. His disposition has not yet been agreed-to, while he receives a stipend and resides in his residence of the Primatial Cathedral in Washington. He was retired by the Synod, but is seeking another assignment "appropriate to his episcopal office." It seems ROCOR had sought his transfer, but after a meeting with the OCA's leadership, that plan was abandoned.
There is another thread on "OC.net" with more information.
His essentially forced resignation has received poor reviews outside of the OCA; Patriarch Kyrill's letter of congratulations to Metropolitan Tikhon, noted that he should correct the problems related to his predecessor. Although he does not recognize the OCA's autocephaly, but does recognize its canonicity, it has been reported that Patriarch Bartholomew was aghast at the treatment accorded to their primate by the OCA's Holy Synod--this may account for why no one from the GOAA officially participated in Metropolitan Tikhon's enthronement. After the resignation, a second hand source told me, while in Russia (or perhaps Ukraine), a cleric in the leadership of the Patriarchate of Moscow asked a visiting OCA official to hand him a book that was on a shelf. It was "The Rudder." The Church of Russia official asked the OCA representative, "Where in here does it authorize you to treat a Primate, as you treated yours?" (Details of this story are sketchy to protect the source.)
While not exactly analogous, Metropolitan Jonah's disputes with the balance of the Holy Synod and the administrative organs of the OCA, are akin to the problems Archbishop Spyridon experienced in the GOAA during his 3 year primacy, 1996-1999.