This is probably because of toolbar data. My browser homepage was mysite.com/myadminpage, without analytics and without adsense. Randomly it seemed, it was one of the top pages in G webmaster tools. The Google toolbar is the only way that Google could have known this page existed.
Since uninstalling the toolbar and basically ridding my system of anything Google and only using Chrome for testing purposes, the myadminpage that is my homepage has completely disappeared from my WMT account.