I've noticed a lot more URLs not being automatically cleaned up since NGS, the pre-NGS URL cleanup code was a lot more reliable, so we've missed something somewhere. I've tried to figure out how people are submitting the URLs, but it's quite hard to reproduce consistently.

One way (reproducable in Opera 10.10/OSX for me):
Open a release and relate to a URL
Select "Amazon ASIN" as the relationship type
Click in the URL field
Use cmd-v to paste www.amazon.co.jp/dp/tracks/B0000AFOPB/ref=dp_tracks_all_1#disc_1
Press enter

Another (reproducable in Epiphany/Linux for me):
Open a release and relate to a URL
Use middle click to paste http://www.amazon.co.jp/dp/tracks/B0000AFOPB/ref=dp_tracks_all_1#disc_1
Press enter

Another (reproducable in Opera 10.10/OSX for me):
Open a release and relate to a URL
Select "Amazon ASIN" as the relationship type
Paste http://www.amazon.co.jp/dp/tracks/B0000AFOPB/ref=dp_tracks_all_1#disc_1 somewhere and drag it into the URL field
Press enter

Result: The URL will probably not be cleaned up in time and the original URL (with http:// added if necessary) will be submitted.