The first definite sign we got came much later, from the Cuthbert's examination of Ganeth. This didn't inspire optimism and joy, and Plant Dude's later warning that Ganeth might not survive an examination on a Lawful Good altar (such as the ki-rins') was a further indication that all was not well.
Some time later, Nomistrus, the head priest of the Temple of Hollerith, ran a series of non-intrusive tests on Ganeth, using True Sight and the like. He reported that, apart from the scads of extraplanar influences on G's spirit (including Plant Dude, canaries, dragons, spiders, whilgs, and others that defied identification), there were three spirits coinhabiting G's body. We knew that the second spirit was the surviving shard of Lessania (one of Ganeth's predecessors as Red One), which had been grafted on to G's spirit, but who was the third? (And who'd mined G's mind with traps to snare people who looked a bit too closely?)
During the Shadowing, certain barriers that...something...had constructed within Ganeth's mind vanished, and Lessania awakened somewhere in the back of Ganeth's mind. Shortly after the Shadowing lifted, before the barriers could be re-established (if they could be brought back up at all after Lessania woke), the ki-rin examined Ganeth to see what was going on with his spirit. They found that some of the loose edges of Lessania's spirit fragment, which were supposed to be bonded to G, were instead attached to a source of pure chaos, which was still small, but growing. The chaotic energy didn't bear any particular signature, leading the ki-rin to speculate that this is being caused by something more powerful than the Chaotic beings G has thus far interacted with (such as Plant Dude, Hajmola, or Nuket). The ki-rin didn't think the chaos source posed a threat to Ganeth, but given time, it could develop into a threat to those around him...
By the time the party reached the Cloudlands, the chaos source had grown considerably. According to the titan King Tizhalux, it had "more energy than a mortal could possibly hold" and could produce a pretty good bang if it were to be released explosively (possibly as a Chaotic Holy Word or some sort of astral explosion); there might also be enough there to fuel a chaotic avatar. The King and his grey slaad pal, called the Pearly One, bled off about ten percent of the energy to stabilize things a bit, buffer Ganeth's strength and constitution against drains (and aging), and enrich themselves (of course), but it was still a big pile of energy, and extraplanars were starting to notice.
When G became mentally paralyzed during his abduction by the Consortium, something else came out and did some serious damage to the Consortium operatives on site.
The chaos source was expected to detonate at the climax of the Dustplane mission, but the party was able to destroy the plane without tapping its energy. Ganeth's anonymous sponsors within Whitemoon placed seals around the source to prevent it from interacting with his infernal body; these seals were also expected to impede future manifestations of the chaos entity.
When Ganeth was transferred to a new body (reinforced with upper-planar snow), Lessania became better integrated with G's spirit, though we don't know what consequences that has. After G was hit by an illithid's psionic attack, the Red One (or something) attempted to manifest but was unable to wrest control from Ganeth. In retrospect, it seems that all of the Red One's known appearances followed successful mental attacks.
During the body transfer, a 25 effective HD astral scorpion of sharpness materialized out of G's energy pool. According to Nomistrus, those 25 HD didn't make a noticable dent in G's energy tally.
Whn the party visited Silverton and the Underdark in the wake of Rakni's defeat, Ganeth was upgraded to a "Level II Threat to the Prime Material" and taken into custody by the Alliance for Law. Apparently this classification relates to the proportion of available energy that's tied to G, and it's a decent fraction. (The mildest threat is Level I, but according to Mountain Breeze, that covers several large-scale disasters.)