It's hard to keep everybody happy, but if a regional leader gets annoyed with the leadership, it's an easy thing for him to go over to the other side. Then there's the logistical situation. Southern Sudan is not the easiest environment in which to choreograph the mass movement of men, machines, and supplies. Essentially it's a basin, and every spring it's engulfed by the rains that fall on the surrounding hills. The waters eventually flow together to form the White Nile, but in the meantime they swamp all the low-lying territory around the rivers.
Road maintenance is a nightmare.
The government forces don't even leave the dozen or so fortified garrison cities any more-they'd get bogged down, surrounded, and annihilated pretty quickly. In some cases they've mined themselves in. Their main objectives lie in Eastern Equatoria. If they take the capital, Juba, they could basically declare independence and nobody could do much to stop them. Juba's a vulnerable city-it's surrounded by the rebels, it's supplied by airlift, and if the SPLA took a few strategic hills, it could shell the airport and probably starve the government's garrison out.