I've entered a few pencil marks, and now Sudoku won't find the solution - why not?
A. The built-in solver uses the same pencil marks as you do. This is so you can assist the solver if it gets stuck, but it means the solver will never add pencil marks to a cell if there are some already present - otherwise it could undo eliminations made because of your superior logic. The downside of this, is that if you enter any pencil-marks into a cell, you need to enter all of them. The easiest way to do this is with the "automatic-pencil-mark" button. If any cell contains incomplete (or incorrect) pencil marks, the solver may not be able to find the solution.