I'm experiencing this issue in 1.12, and it was confirmed by matt on this forum thread:

http://forum.piwik.org/read.php?2,84935,105947#msg-105947

I'm trying to setup a custom segment filtering Downloads to show only mp4 files. When viewing all visits, there are dozens, but when I add a custom segment setting the Page URL contains '.mp4' I get zero results. I'm using the fancy segment UI to build the segment, but obviously something is not working right. One other point of note is that I'm loading all of my data from Apache log files, rather than JavaScript using the included python script.