There aren't many philosophical differences between ISKCON and the Jiva Institute. They both believe in Chaitanya Mahaprabhu's philosophy of Achintya Bhedabheda. And Babaji Satyanarayana Dasa, the founder of the Jiva Institute, is a former ISKCON member, as he describes in this web page:
I never made any propaganda against Srila Prabhupada, ISKCON or Gaudiya-Math, either through internet, through writing books, articles, or by speaking. On the contrary, in my books I have honored and recognized Srila Prabhupada as a propagator of Gaudiya Vaishnavism.
I left ISKCON, or rather, was forced to leave about fourteen years ago because of some philosophical differences. Having philosophical differences is common any spiritual organization, and this is certainly also the case in our Gaudiya Vaishnava history. The beauty of Vedic Culture is that one can have differences of opinion and respect simultaneously. In fact, our very philosophy is based on the principle of difference and non-difference simultaneously. For the modern mind this seems absurd, and any difference is taken as disrespect and inimical. I tried to reconcile one of the differences I had with ISKCON in my book, “In Vaikuntha not even the Leaves Fall”, so that ISKCON’s teachings could be in line with the teachings of the Gosvamis, but this was not acceptable to the ISKCON leadership. As a result I was mistreated and my book was banned. Thus I saw no possibility of reconciliation, although that was my heart’s desire.
Even though I was defamed and mistreated, I did not endeavor to harm ISKCON or the Gaudiya Math. I have never stepped into ISKCON territory after my departure from ISKCON to avoid any conflict or confrontation. At the same time, curiously many ISKCON leaders over the years approached me privately for philosophical advice and consultation and used the material they received for their own projects – often without mentioning my name which was blacklisted in ISKCON. I was and I am still open to peaceful dialogue.”
In any case, one prominent philosophical difference they have is that ISKCON believes that Jivas sometimes fall from Vaikuntha into the world of Samsara if they do bad deeds in Vaikuntha, whereas the Jiva Institute believes that Jivas who dwell in Vaikuntha never fall from it. This difference is discussed in great detail in Babaji Satyanarayana Dasa's book "In Vaikuntha Not Even the Leaves Fall", which you can read here.
Another thing to note is that ISKCON has a sharply negative view of the Jiva Institute, described in this editorial from the ISKCON publication the Sampradaya Sun. They put Jiva Institute people in the general category of "Babajis" who have the potential of leading ISKCON novices astray by overly focusing on the romantic Lilas of Krishna in Vrindavan, which can lead the novices to material temptation. They also characterize Jiva Institute people as "Asampradaya" or lacking a proper Sampradaya. Which brings me to the final difference, namely a difference in Guru Paramparas. Here is the ISKCON Guru Parampara:
- Jaya Tīrtha
- Brahmaṇya Tīrtha
- Vyāsa Tīrtha
- Mādhavendra Purī
- Īśvara Purī, (Nityānanda, Advaita)
- Lord Caitanya
- Rūpa, (Svarūpa, Sanātana)
- Raghunātha, Jīva
- (Baladeva), Jagannātha
- Bhaktisiddhānta Sarasvatī
- A. C. Bhaktivedanta Swami Prabhupāda
And here is the Jiva Institute Guru Parampara:
Both ISKCON and the Jiva Institute trace their Guru Paramparas to Chaitanya Mahaprabhu, the founder of the Gaudiya Vaishnava sect, but ISKCON's Parampara traces its origins to Chaitanya Mahaprabhu's shishya Rupa Goswami, whereas the Jiva Institute's Parampara traces its origins to Chaitanya Mahaprabhu's shishya Gadadhara Pandita. It's also worth noting that the Jiva Institute claims that Rupa Goswami received Diksha from Gadadhara Pandita; see this web page.