Big traffic change for top URL WMT Message
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Hey,
You didn't say in your post, but when you refer to the traffic numbers you are looking at in Google Analytics, are you looking specifically at Google organic traffic?
If you aren't seeing a decrease from Google organic traffic in Google Analytics, then my initial reaction would be to trust Google Analytics traffic data over a message from Google Webmaster Tools. If you have some kind of secondary analytics tool (even something like AW Stats installed on your server) that could be helpful to look at as a double check to make sure you've not seen a drop in traffic from Google.
The other thing I would like at is your top pages that get traffic from Google organic searches. Have any of those pages dropped? For instance, your home page might have experienced a large decrease in traffic from Google organic which could indicate a problem there.
Hope that helps. Thanks,
Matthew