The only way to fix this for me has been to sit in front of a guitar instructor that plays the drum or watches me and tells me when my timing is off and shows me why. This is finally helping me even though progress is slow.
Could I get this kind of one on one help from a website? Not really. I use guitar tricks for their superb song collection and their instructors who will answer any question under the sky about learning, equipment or playing music. These guys are pros and are very cool.
GT has videos on techniques such as pinch harmonics that I use for improving specific songs which are also on the GT site (like Sweet Home Alabama). I've finally improved enough to undertake artist studies that GT has as well.
In short - GT is awesome and keeps me going with videos and pro level tabs and helpful instructors that you can hit up any time for any questions. But I needed a private instructor to fix some of my serious playing issues that can only be addressed in person. Your mileage may vary.