I guess they're as different as they are from themselves versus the Burmese, except a lot of them tend to be Christian. But there are a lot of Buddhists. The Shan are Buddhists, and the Mon.
Depending on what's in their area and how they are making money.... In Shan state there was a lot of opium and now there's a lot of methamphetamine. Some military commanders don't want that to be shut down because that's how they're making money. Others want to protect their own natural resources from the Burmese so that they can sell them.
I don't know of other issues that they're disagreeing on, but it's probably political. There are even maybe border disputes between ethnic states because the people are interspersed along the edges.