I'm not a GWT expert but as you haven't gotten an answer yet I'll give it a go...
The data are not "wrong" (the data is the data) but both these systems (especially GWT) may be estimates in some situations. I think for newer, smaller sites, this estimating can result in 25% swings like you describe.
But more than than, GWT and GA measure different things, so if they ever match exactly that's sheer coincidence.
GWT gets its data directly from Google's servers. GA gets data from users' browsers, later, when your site's page loads.
This GWT tool is meant for optimizing your search presence, not tracking traffic, so use your Google Analytics for that. But no technology to date can track each individual person hitting your site. All these analytic reports must be taken with a grain of salt.