I just went through this same issue, in my case it was because the positions that I was providing to the decoration weren’t exactly aligned with the node. These dev tools https://github.com/d4rkr00t/prosemirror-dev-tools helped me a lot in terms of understanding the document structure and node positions.
Before that I was fudging the decoration positions back and forth +/- 1 until I got them to show up in the update parameters.