Two possible reasons:
1) The "Send to" option was used to "send" the file from FCP to Xport
2) The frame-rate of the source is 23.98 instead of 24.
Both the above will cause audio to be unusable.
If the QT file is at 23.98 convert it to 24fps. The best method for this is to use Cinema tools to conform image and an external audio application to conform audio.
In FCP/Compressor these conversion may be performed using any of the methods mentioned below to convert the 23.98 source QT to 24:
1) in Compressor – using the frame-rate controls option (see attached screenshot). But I can’t tell you whether the quality is acceptable
2) The other - in FCP – change the SEQUENCE time-code (Edit timebase) to 24 BEFORE exporting the sequence… to ensure that the SEQUENCE is at 24fps.
3) The third option - in FCP – change the frame-rate during the EXPORT process – using the “Export using conversion” option and chose the frame-rate as 24.
You could test all options and find the best output of 24p material and then use that true 24p quicktime file to convert to DCP using Xport. I won’t be able to tell you which of these is the best way to convert from 23.98 to 24.