I have no plugins or anything in the Output strip.
I am shortening and rearranging one song from the Tropic Thunder soundtrack CD, so I have 6 tracks that contain bits and pieces of the one song. When I Solo each track, both Input and Output strips read near zero from beginning to end (with minimal variations). But when I play the entire song, the Output levels jump when the playhead crosses one track's crossfade to another, up to +1.2 in the first instance, then it jumps to +4.7 as it moves thru the second crossfade section (this is the biggest jump of all the crossfades), and stays there till the end of the song. The input levels remain near zero. (these crossfades are done with automation. They are a fraction of a second in length and I use 0.0 as my base volume level. They are how I "splice" together rearranged sections of a song). However, if I stop the playhead while it is reading +4.7, then re-start the playhead at the same spot, the volume level on the Output strip drops back down to the normal levels that are consistent with every track when Soloed.
It's like the crossfades and segues, i.e. where there are tracks overlapping tracks, big peaks are created, even tho everything sounds seamless with no big jump in volume while listening on my headphones. And in order to mitigate these isolated peaks, Logic is lowering the volume of the entire song so that the peaks are accommodated.
But its not only volume, it's clarity too. The resultant bounce is much lower in volume, and quite muffled in sound... all the higher frequencies are gone... its a muffled mess.
Whenever I Bounce, there's a Window that pops up with a progress bar - Normalizing. Could the set up/defaults in Normalizing be the prob?