If you apply a fade to an Apple Loop in the Arrange window, the portion of the loop encompassed by the fade will play at the loop's original key and tempo, rather than the key and tempo of the song. This issue occurs with Logic Pro 7.0 and Logic Express 7.0.
The core issue is that Apple Loops do not support fades, so you shouldn't assign a fade directly to one. If you'd like to achieve the effect, export the Apple Loop (in the Arrange window, choose File > Export > Region as Audio file). Then bring the exported file back into the Arrange window and apply the fade to it.
Logic 7.1 and later prevents this issue by disallowing fade application to an Apple Loop.