Logic Pro X Fades Issue?

Trying my first pre-mastering attempt in Logic Pro X. I decided the best way to work was to create "Alternative" mixes for each track on the album totalllying 13, ordering each song as a region. So I went track by track and did my processing and added my in and out fades. Saved each time I switched alternatives to work on the next song.

On return, I opened each alternative and started boucing out. Check the bounced Wavs and three or four tracks had a weird "ghost" of material from other regions in the session. Reopened the Logic session to find that where my fades were, a little nugget of sound was playing from another region in the session.,

Simply altering the fades in any way took care of the problem, but it's not the most elegant solution with an anxious client (eager to hear your awesome masters) next to you and the Discmaker's upload page on the other computer;)

Anyone run into this yet?