Look at the baseline shift value in the Character palette, it should be set at "0" under normal circumstances. If it is set at "0" and this is still happening, then it's probably a font issue.
My guess would be it happens mostly with free or inexpensive fonts. It happens because an unusually large area is included for the descenders in the font, in other words sloppy work by the font author. If this is the case, you're out of luck with those fonts.
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