Nucleon was an unstable but potent energy source developed on Hydrus Four, capable of revitalizing damaged robots and restoring them to (a semblance of) life and health. It was also self-perpetuating, so that a robot endowed with it would never need refueled again. However, its instability created side effects, such as madness, in its beneficiaries.
Grimlock, determined to resurrect his Dinobots and fellow Autobots on the Ark, used nucleon anyway (after testing it on himself). However, while the other Autobots seemed merely restored, Grimlock began to have periods where his systems would lock up (such as his fist freezing in place). Ultimately, he froze in place totally after the battle with Unicron, only to be reborn; as a powerful but non-transforming robot (an Action Master).
In the short story "A Distant Time and Place," however, nearly all the resurrected Autobots were rendered unable to transform. Later, a nucleon-purifying process was developed, which Grimlock acquired after foiling an attempt by Bludgeon to resurrect Megatron using the improved nucleon process. Using that, all the Autobots were able to regain and/or ensure their ability to transform. It is hard to say whether this is canon, as Bludgeon and Megatron both die (although the latter was bathed in nucleon), but this would explain how Prime and Grimlock are "normalized" by the time of the Generation 2 comic.