When Yaroslav Popovych, riding for the Discovery Channel Pro Cycling Team, rode away for victory, rumours spread that Freire had been ordered by Rabobank not to ride for the victory, to secure help from the Discovery Team in the mountains. Although rumours were denied by both teams, Freire was upset after the stage. Freire continued his successful year by winning the Vattenfall Cyclassics ahead of German favourite Erik Zabel. Freire had half of Rabobank's victories in 2006. His season was cut short by neck and spinal injuries, forcing him to miss the Vuelta a España and world championship. Freire re-signed for Rabobank in late 2006 until the end of 2008, rejecting Saunier Duval-Prodir.