To clarify the confusion:

The Jovians have for some time been suffering from the 'Jovian Disease', a genetic disorder that came about through their excessive use of genetic-engineering (not from the EVE gate radiation....I don't even know why you would think that). The disease Became more and more prevalent in the past 200 years, and is a major reason for the Jove absence from the current political stage in recent times, along with the Enheduanni threat.

REAL BACKSTORY: When the Jove set off to build their empire after the collapse of the EVE gate, their massive ships were filled with 'sleeping' jove, as well as the Enheduanni, or 'Architects' if you prefer. The job of the Enheduanni was to ensure the survival of the sleeping Jove during their centuries long journey. The Enheduanni were once the lowest class of citizen within the empire. As the empire progressed, and the 'sleepers' became more important due to the artificial reality they constructed and could run scientific experiments in virtual conditions much faster and precicely than in the real world, the Enheduanni became tasked with maintaining them, managing their occasional transfer between their virtual world and their real bodies, and gathering the scientific knowlegde that the sleepers obtained during their virtual experiments. The Enheduanni, however, began hoarding information and technology from the Jove, using knowledge that should have been for the good of all, to advance their own agendas. Meanwhile, the Jove disease was beginning to kick in, and the Sleepers began to realize they were being used by the Enheduanni. The Jove pushed the sleepers to create a cure for the jovian disease, but the Sleepers refused, likely because they believed the Jove were using them as well. The sleepers eventually fled to what we now know as Wormhole space, and the Jovians were left to essentially die.

Present day: It is unclear what the fate of the Jove is, but most people assume (due to information given BY jovians about the disease) that the disease has claimed the lives, or at least sanity, of most or all the remaining jovians. Likely all that remain to defend the jovian borders are their virtual consciousnesses, which likely still control basic activities within Jove space, but have no influence outside of it. The fate of the Enheduanni is in question. If they also had the jovian disease (them being, themselves, jovians), the Enheduanni might be gone as well, or may have become something else entirely in their quest for a cure. Nobody knows.

THE SLEEPERS: Are still very much alive, but without the Enheduanni to bring them out of their simulated world, they sleep forever. Inside their virtual world, however, they have created what the call a 'technological singularity', a universe within which anything is possible, they exist peacefully in the pursuit of infinite knowledge. Their world, however, was being torn apart when people from New Eden started exploring the sleeper enclaves, and taking sleepers to harvest their implants. This caused serious reprocussions for the first generation of clone soldiers, who occasionally had a sleeper consciousness return to the brain VIA the implant, causing the soldier to go insane (2 consciousnesses within one head will do that). Since these initial failures, the empires have developed their own technology based on the implant, and the harvesting of sleepers has ceased.

The sleeper / talocan destruction: When you see the great wrecks of sleeper enclaves and talocan ships in wormhole space, what you see is the damage caused by the internal war with the 'Other'. Within the sleeper world, to which all individual enclaves are connected, there is a simple rule: Every consciousness within the virtual world must have a body to return to. Within this virtual world, however, an artificial consciousness was formed, which they called 'the other'. In essence, a malicious AI, the other spread throughout the sleeper virtual world and caused a great deal of damage, resulting in quarantines to try and contain it, and the physical destruction of enclaves and ships in space as the sleepers and their space faring drones tried to contain the infection (The Talocans had some part in this, though it's unclear what).

I'm a little muddy on some of the really specific details, but this is the actual story behind these 3 groups I believe.