Why are certain episodes highlighted in blue?

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Those are 'related' messages, i.e. ones related (usually by having matching subjects) to the selected message.
In Lion, that setting is in Mail's Preferences (in the Mail menu) > Viewing, in the section "View conversations:", the item "Highlight messages with color when not grouped". Unchecking that item will turn off that highlighting; you can also change the color used for that highlighting by clicking the box at the right end of that item.

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