The Flanders-Wallonia division is economic if anything. Historically, Wallonia relied on its coal and iron industries, but after the war the coal production pretty much stopped. Now, Wallonia is suffering from very high levels of unemployment and it has a significantly lower GDP than Flanders. Of course, Belgium puts a lot of money into development projects for the worst regions, but the Flemish see this as all of 'their' tax money going to the Walloons. The language divide makes it worse, as it's a lot easier to get an "us-vs-them" thing going.
Still, Indonesia has its own problems too, with the south Moluccas and Papua.
That division of Eastern people, namely Maluku (Moluccas) and Papua is mainly religious conflicts, a thing so old and abandoned in their homeland of Europe.
Aceh (western most Indonesia), is an autonomic province, granting them full control about their own governance and law. They chose shari'a and strict Islamic code. They proudly call their land "The gate to Mecca."
East Papua (eastern most Indonesia), which is split from Papua (into East and West), rejects all Islamic spread and influence. They seek to deny their activity there, which is granted by the central government. They are strict Roman Catholics and proudly call their land "The gate to Jerusalem." (instead of Vatican city)
Same reason with Southern and Northern Maluku. Unlike Belgium, people here have been involved in bloody violence until the government divided them into two separate province. The Northern one is now free to apply their own Shari'a law, where the Southern Christians aren't subjected to no longer.
Separatists often argued about Islam dominance in our government, thus it can never be fair to them. So they keep seeking independence, which can be quite a mess, really. Probably, after they are done with their very own Republic, they'll start ousting Muslim minorities or worst, started purging them in Srpska Republic style. Which would call more violence within the border. Most people lost sympathy for them after witnessing the degree of violence involved there (e.g. gutting pregnant women).
