martinibuster - 9:08 pm on Mar 23, 2010 (gmt 0)
but in my Google webmaster tools section under links pointing to my site, Google has them listed.
It feels as if this has been discussed in the link dev forum at least a hundred times in the past year. It seems as if this comes up at least once a week. There is a huge misunderstanding about this. So here we go... again. ;) I'm going to have to put a sticky about this so we stop repeating this answer over and over again.
Google has always shown samples. Even the WMT tool results are only samples. That means it shows links that count for ranking and links that do not count for ranking. This has been the case since Google began showing backlink data.
I hope this clears up the misunderstanding about what your WMT results mean.