Thanks for the feedback!
We are aware that FlipPix works slightly differently from most other nonogram games. Most nonogram games do not give you any feedback as to whether you are going in the right direction or not (until you successfully solve the puzzle), and we find that that frustrates many people, particularly those who have never played nonograms before. Our way does have the disadvantage that it makes the more difficult puzzles harder to solve (since you cannot experiment by temporarily marking the squares that you THINK might be clear). In fact, we generally limit the difficulty of the puzzles to those that can be reasonably solved using this interface.
We have considered adding an 'Advanced' mode which would work in the more traditional style that you describe. However, we have not gotten a lot of call for that so it hasn't been a priority. I personally would like to see it, as it would enable us to include some of the more difficult puzzles that we have had to discard in the past.