I knew tonnes of chords, but yet I couldn't actually get from the start of a song to the finish line without stumbling over a chord change at one point or another, or perhaps many :-)
For me, the breakthrough came through when I discovered Guitar Principles, and specifically when I bought their book "The Guitar Principles Path, Level 1: Chords & Rhythm". This book saved me. It didn't crap on about the usual stuff that chord book crap on about. It actually spoke about the Technique involved in fingering chords, and then gave me a solid consistent method of learning how to change back and forth between chord shapes.
I highly recommend it. You will find it at www.guitarprinciples.com. Check out their free essays while you are there too - all are invaluable to a guitar student.
Have fun
Trevor
www.flyingfingers.ie