One oftenoverlooked element in Logic is the Master Volume. This is an additional fader after the Master Channel Strip that can apply an offset to the mix (very useful for surround mixes because it applies to all 5.1 channels equally).
Sometimes (by accident), this channel is not at unity gain (0dB) and the level of the bounced mix is off by that amount.
The Fader is at the right lower corner of the Navigation Bar. It can be hidden with a checkbox in the "Customize Transport Bar" window.
Hope that helps
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