This game is definitely interesting. I like it.
I've never done a paper Sudoku - so, I'm not sure if your grid/mapping engine has a bug in it. Each sub grid (in a certain direction) contains the exact same elements as it's sister grid.
In other words - figure out three (differentiable, but simple) patterns. Once you do this, you need only match the SIMPLE pattern (rather than trying to fit the long patterns within each other)