I've received several emails asking about this, so I'll go ahead and post the answer here.
In addition to the normal points you get for clearing a pair of tiles, there are also bonus points that are being added up and awarded when you complete a level.
These bonus points are based on WHERE you removed the tile from on the board (well, the truckbed). Tiles removed from the bottom of the screen are worth more bonus points than those removed from the top of the screen. There are 12 potential rows on the screen and each row has it's own set of bonus points. So if you can clear a screen pretty quickly before the tiles move up very far, you will get a much larger bonus.
These points are awarded for EACH tile based on where it is. You do not have to remove two tiles from the same row to get the bonus. For the sake of simple math, lets say the top row tiles are worth 10 bonus points each and the bottom row tiles are worth 120 bonus points each. If you remove a matching pair where one tile is on the top row, and the other is on the bottom row, you get 130 bonus points. If both were on the top row you'd get 20 bonus points and likewise if they were both on the bottom row you would get 240.
These values also climb as you go to the higher levels. So the top two tiles are worth a lot more bonus points on the 99th level than the ones on the 1st level in the Quest Game.
Hope this explains it well enough.
