looking for story where john's family think he is a disgrace, unaware that he is in command of Atlantis. they either come to atlantis or become aware of what he does somehow. long stories are better.
I found two more and they're not quite what you're looking for but they are pretty close. If you haven't read them they can tide you over till someone comes up with something better.
The Bobby Newman Factor http://clockstopper.livejournal.com/13439.html
Glass Houses by MistoKitt http://www.wraithbait.com/viewstory.php?action=printable&sid=11508&textsize=0&chapter=1
These don't fit your request exactly, but I thought I'd point them out.
A list of stories that involve John's ex-wife and his father. There are a few where they find out about his promotion. A link at the bottom leads to another list involving his brother. http://laughtersmelody.livejournal.com/33321.html#cutid1
This is a Big Bang fic, Guardian by Tarlan. It's an AU, where John is offered Antarctica or resignation, and he chooses to resign. He spends his time flying people from his dad's company around. He meets McKay, things happen, and he ends up in a coma in an Ancient outpost in the Bermuda Triangle at the bottom of the ocean after a crash. Along the way his dad and brother find out about alien tech. Sheppard/McKay slash. http://sgabigbang.talkoncorners.net/?view=fic&id=66
no subject
Date: 2010-12-28 12:35 am (UTC)http://www.fanfiction.net/s/4068099/1/Mr_Sheppard_Goes_to_bWashington_b
Paging Colonel Sheppard by Quasar
http://www.wraithbait.com/viewstory.php?action=printable&textsize=0&sid=12790&chapter=all
no subject
Date: 2010-12-28 12:46 am (UTC)thanks
no subject
Date: 2010-12-28 01:12 am (UTC)The Bobby Newman Factor
http://clockstopper.livejournal.com/13439.html
Glass Houses by MistoKitt
http://www.wraithbait.com/viewstory.php?action=printable&sid=11508&textsize=0&chapter=1
Here's a couple for you
Date: 2010-12-28 02:24 am (UTC)My Brother can Kick Your Brother's Ass (http://www.fanfiction.net/s/5194765/1/) by Sqweakie
Blood's Thicker Than (http://www.fanfiction.net/s/5461786/1/Bloods_Thicker_Than) by obsessed1
and
Blood is Thicker (http://www.fanfiction.net/s/4138921/1/) by T'Pring
Re: Here's a couple for you
Date: 2010-12-28 12:40 pm (UTC)Dave is captured by the Trust instead of Sheppard. He finds out about John's work when John is captured too.
no subject
Date: 2010-12-28 12:54 pm (UTC)A list of stories that involve John's ex-wife and his father. There are a few where they find out about his promotion. A link at the bottom leads to another list involving his brother.
http://laughtersmelody.livejournal.com/33321.html#cutid1
This is a Big Bang fic, Guardian by Tarlan. It's an AU, where John is offered Antarctica or resignation, and he chooses to resign. He spends his time flying people from his dad's company around. He meets McKay, things happen, and he ends up in a coma in an Ancient outpost in the Bermuda Triangle at the bottom of the ocean after a crash. Along the way his dad and brother find out about alien tech. Sheppard/McKay slash.
http://sgabigbang.talkoncorners.net/?view=fic&id=66
Maybe?
Date: 2010-12-28 11:25 pm (UTC)http://archiveofourown.org/works/1722
http://archiveofourown.org/works/2512?view_adult=true