My situation may be similar.
I have two Ubuntu gnome systems, one desktop and one laptop. Both have Apache installed in the default location of /var/www. On both I set myself to owner, and sometimes www-data as group.
I was perplexed that, using Nautilus, I could not delete file on the desktop using the delete key, but I could on the laptop. The desktop required right-clicking, and choosing delete. I later find out shift-delete would work, and neither method used the trash bin.
After much hair-pulling (well, not that much, as I don't have much), I realized the difference... my desktop has /var mounted in a separate partition.
It seems that Nautilus won't move a file to trash from a different partition, possibly only if you are not the owner of the root of that partition, so it can access the trash file on that partition. I don't really want to be the owner of the /var partition, so I never tested this out. Perhaps there is a way to mount the partition that would allow it. There is some discussion about a similar problem on launchpad.
One problem with having a trashcan outside the user's directory that is r/w by normal users may be that other users may be able to see each other's files.
I hope at least to point out the possible reason, if not the solution.