In the ALT+L Options, if u set a min of 0 users, then the channels with 1 user doesn't appear in the Channels List, but if u set a min of 1 user, they does.. another fact is that, if u set a min of 1 user, when u reopen mIRC, it is set to 0 again...
I think it's not a problem with the server.. the thing is... if u set it to 0 and u click on Apply it does show the channels with 1 user, but if u set it, close the dialog with OK and make a /list it they doesn't appear... unless u do a /raw list
I have experienced slightly different replies from a server when using either /list or /raw list. /raw list usually returns more information such as channel modes, though this maybe specific to certain servers and depends on what they support.
Some servers will have a setting which allows the administrator to force the server to hide channels with fewer than a nominated number of people in them, this may apply in your case.