This happens when a stereo audio file is played back on a mono audio track. When playing back a stereo file on a mono track, Logic Pro automatically adapts the level. Thus, bouncing results in a corrected level. When using Digital Mixdown for a stereo file on a mono track, the stereo file will be converted into a mono file. This means that the level of the left and the right channel are added.
To avoid this when using Digital Mixdown, make sure that the file type (mono/stereo) matches the track setting. Alternatively, you can use the bounce function to merge stereo audio Regions into a mono file.