If handles have not slipped, and are bolted properly and the SS part below is fine, then the only thing this could be is the line between the handles. The way the tandem handles work is one side of the rudder runs to one handle (lets say the rear) and the other side of the rudder runs to the other handle (say the front, but through a pulley forward of the handle). All that's left to complete the loop is a line from one handle to the other. If this line is too long or short the handle are not in sync.
My first TI, after a sail in strong winds went out-of-sync and I found after loosening the rudder lines in the rear, I could remove one end of the line between the handles and add a single overhand knot to "eat" some line. It wasn't perfect, but tightened over the next few sails to good enough. If you do this, check both ends of that line to be sure the line and it's loops are in good shape and not failing, causing your problem.
- - - - - Hobie Island Sailing since 2006 - - - - - 2011 & 2012 Hobie AIs and a 2012 TI