This happened to my site a year or so ago. I couldn't figure it out. One high powered site linked to an internal page on my site, and that was apparently enough to make that page the one with the highest rank. The only other links going to that page were internal links, and only about 4 or 5 of them.
I was experiencing other problems with this site at the time, (-950 penalty, lots of supplemental pages), so I figured the issues were all somehow related.
After about 3 months, WMT indicated my home page was the top ranked again. The site also came out of the -950 penalty as well, so I still don't know if the two were related or not.
I don't know if this will be of any help to you or not, but it's possible this could be an indication of other issues with your site, or possibly when a high ranking trusted site links to you, it shocks the Google algorhythm for a few weeks, and it takes time for things to settle down again.
No problems since on my site, other than my traffic is still just at 81% of its peak prior to all the problems.