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Okay, I just got CS3 and I'm doing this wicked big pixel art thing. You know when you have two different colors touching each other and you use paint bucket on one, it will only fill that color? When I do that, photoshop just flood fills the entire colored area on the layer, not just that one color as it's supposed to. I tried using the magic wand tool, which should select only the color you clicked on, but again, it selects all of the colors as one object on that layer. I checked- I'm not on a different layer, I tried it with transparency on and off, and I have no idea why this is happening. Any help?
Look at your tolerance, perhaps it is set at 255?
The default value is 32 and when drawing this should prefent PS from filling in existing colors which fall outside this tolerance. I.e. if the two colors are both uniform you could lower the tolerance to 1 or 2 and it should work fine. If there is some anti-aliasing going one, the tolerance needs to be set a bit higher.
If this doesn't help, you could always select the color using menu Select - ColorRange and then pick the color. Again work with the tolerance setting in this dialog to get the selection you want.
The same goes for the magic wand tool btw, which imho is the worst tool one can use for selecting, unless colors are absolutely uniform.
Hopes this helps.