Ok I've two web site http://www.SubmitSeoArticles.com and http://www.NcrPropertyDealers.com both of them are on same server and have link to each other but in google webmaster it shows other site as linking to my site but not these two sites?
If your on a dedicated IP and those are the only two sites that would lead me to believe that Google is definitely discounting your cross linking scheme. If it's on a shared server with hundreds of websites the odds are lower, but it's still possible. It could also be that your backlinks havent been updated lately.
There's no problem having multiple sites on the same server, as long as none of those sites get penalized or else, the others might be affected too due to having the same IP's. As for backlinks, Google normally don't show them in GWT and to the public.
Maybe the report isn't in real time? What the time difference between you added the backlink and checked the tool?
Backlink means sites which are pointing to your site and tool is to check within google webmaster module to list such sites.
What theentry is pointing out to you is that the tool is not instant. If you only added the links yesterday for example, don't expect Google Webmaster Tools to show the links between your two sites. Also Google looks at far more information that simply whether the two sites are on the same ip/server. If you use Google Analytics do you have both sites set up in the same account? That tells Google that you own both sites. Do you have the same registration information added to both domain names? Google will know this too. If Google beleives that you own both web sites then it is highly likely that they will discount the links between your sites especially because they are not related.
Google's LINK: operator output and WMT only show a "sample" of your inbound links that they know about... and usually a VERY small sample. They even show links that don't help your rankings like NOFOLLOW links and links from URLs known to be under penalty. The point is that they do not want you to know which links they have found, which they haven't, which links count, which don't... If they did show you all of your links it would be relatively easy to reverse engineer the link dependent portions of their algorithm. There is nothing wrong with having two sites on the same IP that you own interlinking with one another. This is perfectly natural. Now... if you interlink 50, 100, 200 sites of your own (regardless of whether they are on the same IP or not) then you will likely raise eyebrows at Google. These are typically link farms which ARE a violation of Google's Webmaster Guidelines and can result in penalty. But 2? pfft.... no worries.