Comments not showing up when "inline comments"

Take a look at the review: https://www.limewire.org/fisheye/cru/LWCR-530 . Comments on some files (such as RRProcessingQueue) aren't showing up as inline comments – they only appear when viewing comments above the file. This is a major issue for us. The review is generated by uploading a diff -u patch.

I had thought the pattern was with fully deleted files – but I tested it out on another review (also from a diff -u uploaded patch), but those show up fine. I'm not sure what's unique about this review, but something is going very wrong.