I'm using subdomain module for groups, the subdomain name is supplied by the user from edit form. Everything works fine.
But if you load node(group with subdomain) from some code with node_load() and then save it (even without any changes) with node_save(), the subdomain for this node will be dropped from table.
The problem is, on my opinion, that in $node object there no parameter related to the subdomain, so when it saved it saved without it.