you can specify the domain both for Webmasters and Analytics, if Google Analytics has not the exact domain registered in your account the stats retrieved will be for the latest site added to your Google account.
More info can be found at this FAQ: http://storejextensions.org/faq/why-the-google-analytics-integration-shows-stats-for-a-different-domain.html
and also in several threads in this forum already solved.
In the image below you see parameters in the component configuration to set the preferred domain both for Webmasters and Analytics. Take care that they must match exactly the domain registered in the Google account.