When an Apple Loop is converted into an audio file, the resulting file may not play at the song's current tempo and key settings. Instead, the new audio file will play at the original Apple Loop's tempo and key.
This happens when you select an Apple Loop region and choose Audio > Convert Regions to New Audio Files from the Arrange window menu and you change the "file format" parameter in the resulting dialog window from "Original file type" to either Wave or SDII. This creates a copy of the original Apple Loop file, but without the transient and category tags. That means the file will only play at whatever tempo and key the original Apple Loop was recorded at—not at the tempo and key of the song.
Logic Pro/Express 7.2 resolves this issue by enabling the Elastic Audio feature for exported files. When you convert regions to new audio files, the Follow Tempo box will be checked for the new audio files created.
If you want to convert Apple Loops to new audio files that will use the song's tempo and key settings in other audio applications, select the loop (or loops) and choose File > Export > Region as Audio File. Though this new file will play at your song's current tempo and key, it can't follow subsequent tempo or key changes like an Apple Loop; it's fixed at the tempo and key that your song was set to when you exported the file.