Problem with Dead Spots in track volume after latest IOS GarageBand compatability update

I'm relatively new to Logic Pro and this forum so not sure on how to use either I guess.
Anyway, I recently updated my Logic Pro 9 with the latest GarageBand for IOS compatabilty update and immediately noticed that on one song a track has lost volume in parts and I can't see how.  Other parts of the same track have normal volume. I can't see where the volume could have dropped. I haven't changed anything and the volume is set to 6 for the entire track.
Has anyone else experienced this and do you know of a remedy. The track I am referring to is a track with Logic Strings from the Orchestral String Instruments.

I believe this issue occurs only between songs that iTunes has converted to a lower bitrate for you during transfer to your iOS device and songs that it has not done this for. Take this Between the Buried and Me album, for instance. I have marked all of the transitions that should have been gapless but probably aren't in red. I know for sure that most of these marked transitions are indeed broken and that the most of the transitions not marked in red work flawlessly... I honestly can't remember whether or not some of these transitions were gapless or not, but the many transitions I do remember working or not working match up exactly with whether or not the songs on either side of the transition were also on other sides of the 256kbps threshold, the threshold at which I enabled iTunes to convert tracks to 256kbps AAC.
I'm going to try re-sync'ing my library with that "feature" disabled and see if it fixes my gapless playback problem. Will post the results once I test it out.

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