You've got a couple of things mixed up there, which is not surprising given the amount of misinformation floating around out there.
The sandbox has nothing to do with indexing or links.
It appears to be an "aging delay" that prevents newly-discovered sites from being ranked well. The reason I say "newly-discovered" is that it seems the aging delay kicks in when the site is first indexed, not when the domain is first registered or when the first page is posted to the web.
Your site can be fully indexed, and yet still be under the aging delay. Your site can be old enough to be out of the aging delay, yet not be fully indexed. The two have nothing to do with each other.
Your backlinks in Google will NEVER show a fully-accurate result. The display of results from the "link:" command has only displayed an apparently random sample of the links Google knows about for several years now.
The link information in Google's Google Webmaster Tools
appears to be more complete than that offered by a general search using the "link:" command, but there's no way to tell if it's 100% accurate (I suspect it is not).
In any case, neither of those link-checking methods will tell you whether or not Google "counts" that link in your favor in the first place. The fact that they know about (and choose to display in response to a "link:" command) the link really doesn't mean much of anything...