You guys may have already figured this out, but just in case, wanted to post a quick note. I wasn't sure if Caarrie's last comment was a resolution on flyspray, but seems to me all the dwarves are somehow being linked, which may be Duhh by now, but made sense as I was thinking about it and would rather post something and be wrong than remain quiet and possibly help.
Seems like dwarves are being linked, no unique identifier in DB maybe? It may happen when a dwarf first logs in. When I first logged in, my guild mate saw me as the ghost image. This was my first impression too when I noticed it. I also saw the other dwarfs movements sometimes, even saw them /die in one case. I was thinking something to do with unique identifiers or some sort of mapping in the DB, but you guys would know best. Just thought I'd throw it out there, just in case it helps.
I don't think it is random, I think it is whoever moved last or logged in last, and that triggers all dwarfs to be in that position on the map on the server, until their client reregisters their /pos, and server tries to compensate. I think last dwarf logged in may make more sense. Explains ghosting because of lag between the reregistering and the mining, trading, interaction issues, etc.
I'm on Linux 64 bit version, btw.
Good luck!