I have had my tags munched by itunes in the past when a housemate ran it on my shared folder, it was unable to read the tags so just removed them.
Setting his access to the share to read only solved that problem. Perhaps you have a program that cannot deal with the type of tags you have done?
I would suggest using foobar or tag and rename to make sure there is only one set of tags present, and then see how that goes.