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This can be Style dependant. eg: Swanky where the banner is inserted in a banner if you like. Any change of colours of the image can look as if it's mis-aligned.
Another cause can be introduced code particularly some styling which may have an effect on the specifc style used and the supporting styling which may be inherited.
I doubt if there are any general aspects that would affect all styles.
These are simply based on experience and I guess that I would have to see your site to be able to examine it and see if there's anything that jumps out.
If you are using FireFox then an excellent tool to highlight aspects such as those you are suggesting is Firebug. A free download add-on. It's a GUI based examiner of your site and you can see all the code that affects an element in your page.