I have the exact same problem with the backup stalling on .amazonmp3/pipe at the calculating checksum stage. Seems to me backup has two issues here a) the presenting problem and b) the inability (it seems) to actually select this hidden folder as an excluded folder in the excluded files/folders window. I don't know how the first problem might be solved, but the second might be solved by permitting the actual typing of the hidden folder name in a bespoke manner, rather than via point and click selection from the user folder.
Unless of course I missed something...don't think I did though. I'm not especially concerned with backing up hidden folders and their files anyway. Assume if I needed to restore from backup the Amazon MP3 service could just be reinstalled from the .deb on the Amazon website anyway.
Perhaps the backup tool could be given an option under advanced options to "Ignore hidden folders and files"?