Lots of wood are so coarse grained that they need to be filled.
Having worked with a lot of Walnut however I find it not to be one of them.
From the picture it looks to me that you simply did not sand it flat to begin with.
220?
You have to start with 80, to 120 or 150 to flatten the wood before you finish sand with 220 or up.
The fact that your joints are a problem tells me you never got it flat to begin with or are using green wood?
Having worked with a lot of Walnut however I find it not to be one of them.
From the picture it looks to me that you simply did not sand it flat to begin with.
220?
You have to start with 80, to 120 or 150 to flatten the wood before you finish sand with 220 or up.
The fact that your joints are a problem tells me you never got it flat to begin with or are using green wood?