It's been a lame running joke, started in Dark Crusade and then onto Soulstorm. It's rare, it's stupid, and it's funny.
But it seems that, in Warhammer40K, the IoM is basically a coalition of Emperor-worshipping fanatics who hate each other with a vengence. During the Kaurava System debalace in Soulstorm, the Blood Revan Space Marines battled it out against both the Sisters of Battle. The Blood Revans wanted to exterminate the Kaurava System, and so does the Sisters of Battle, but the Sisters of Battle wanted the Space Marines to be under their command. Space Marines don't want to be under the command of a crazy militant army, and so hilarity ensues. Meanwhile, the Imperial Guard stationed on the Kaurava System didn't like the idea of being exterminated, and so had to resist.
Then you get the Radical Inquistiors and the Puritian Inquisitors. The Purtains are your average "Burn the heretic, the mutant, the traitor" loon, while the Radicals want to use Chaos and Xenos technology...in order to battle Chaos and Xenos. Purtains see the Radicals as heretics, the Radicals see the Purtains as stupid. The result is total chaos.
Then, back during old fluff, a bunch of crazed Inquisitors who believed in the Star Child theory. The emperor will reborn...but he can only reborn if he dies. So, all you have to do is kill the Emperor, and volia, he'll come back to life! Luckily, the Star Child theory has been declared a heresy, but still...
I know, I know. The IoM isn't really that unstable. But it seems so funny if it was.