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First things first, the Shivans are a hivemind (stereotypical excuse for Shivan single mindedness).
My theory involves a 'cataclysm' which separated the Shivan fleets a long time ago (probably the destruction of several Jump Nodes simultaneously). After the cataclysm, the Shivans decided to nuke all other species because they did not want another cataclysm or something. Fortunately, the Shivans had 'backup hives' which come into motion when a fleet (or fleets) get separated from DaBrain.
The Shivans that came from Ross 128 and attacked the Terrans and Vasudans in FS1 were from a different fleet from the one in FS2. They were probably an expeditionary force which got lost after the disaster that separated the Shivans. Their fleet was very small so they decided that they had to create a sub-hive on board the Lucifer. This is why they needed to shield it and protect it so much.
It is to be noted that they are ultimately the exact same Shivans as the Shivans in FS2, they were just separated for a long time (who said that they hated these theories which say the Shivans are different? Mefustae?).
The Sathanes in FS2 were part of a larger fleet, perhaps one of the biggest Shivan fleets separated from the main one. Because the FS2 Shivans had such a large fleet already, they did not need to shield their capital ships like the Lucifer. The Comm Nodes in the second SOC loop were being used to try to communicate other Shivan fleets far away so the FS2 Shivans could join back up with them. The supernova of Capella was used as the gravitational field for the use of a super-jump node so that the FS2 Shivans could join up with some other Shivan fleet (alternatively it could be used as a beacon so the other Shivan fleets could find it, but it seems a stretch that the Shivans would blow up a star just for a signal).
This does not rule out another species the Shivans are at war with, perhaps those who caused the 'cataclysm' in the first place by using a type of super weapon to weaken the Shivans into individual fleets. Or something. Blegh.
Well, anyway, what do you (SG people) think of it?