Some of our avid players find that for the more difficult puzzles, asking for hints over and over can result in the same suggestion for a candidate reduction, even though you might have applied it!
Here's why: (Health warning - this answer may still leave you puzzled, but we'll do our best!)
Astraware Sudoku uses its built-in solver to work on puzzles in progress, and when you ask it for a hint, it takes your current board (values you've entered) and "solves" it from there with the following steps;
1) It copies to its internal grid each of the given values and the values you've entered
2) It fills in all the possible pencilmarks for that grid
3) It removes all candidates for rows, columns, and boxes where that value already exists
4) It works through all of the techniques in order of increasing difficulty until it finds a place where it can make some progress
5) It remembers the 'solution' used and can show up to 4 different levels of hint for each move - i.e. highlighting an area to look in, highlighting a cell to look at, telling you there's a single position or placement, right up to telling you the method and solution if you keep asking enough!
For hints which result in a new value being added to the grid, this is fine, as the next time you ask for a hint, the grid (for step 1) will be different.
HOWEVER, if you've just been given a hint for a candidate reduction (for instance, a "naked pairs" or "X-Wings" item), and you apply that, all you've done is make a change to the pencilmarks on the grid. Unless you then go on to find your own additional value to add in, when you ask for the next hint, it will do the same copy (step 1) as the previous time, and so give you the same hint.
RESULT : The game is seemingly ignoring your pencilmarks for the purposes of giving you multiple hints!
There's a reason for this though; There are two ways of playing using pencilmarks - additively and subtractively.
Players in beginning puzzles, especially written ones in a paper, use only a few pencilmarks additively - that is, here and there when they need to work things out. They don't need to put in all of the possible pencilmarks! If the game were to try to give a hint using a grid that has no pencilmarks in at all, it would not find any solutions, so instead it builds up its own internal list.
For later puzzles (tricky and up) where the challenge tends to be about candidate reduction, players tend to switch to working subtractively - exhaustively filling in the full grid of numbers and crossing these off as the puzzle progresses. In Astraware Sudoku, the auto-pencilmarks option does this for you (and adds a time handicap of 3 minutes because that's about the amount of time it saves.)
In both cases, the game is ignoring any pencilmark changes you make; if it were to give a hint based on your pencilmarks that hint could be incorrect (which wouldn't be great!). We decided that since the vast majority of players are casual players who play the beginner through medium puzzles, it would be better for the hint system to work most easily for them. It turns out that for our daily puzzle players, only 1-2% of people play anything above the medium puzzles!
We are considering making a "Trust My Pencilmarks" option for the relatively few advanced players who still want step-by-step hints, but we would have to put in a warning message that it will only be as correct as your progress through the puzzle so far! If this would be of interest to you, let us know!