The air currents in the closed crawl did not reach the corners = wet. As you closed it, now it requires conditioning by; http://publicecodes.cyberregs.com/icod/irc/2009/icod_irc_2009_4_par111.htm I am not surprised it smells wet and musty, without forced air moving under there. I doubt a few vent holes to the conditioned areas will help much. The rim joists should have been insulated with foamboard, as the walls; http://www.buildingscience.com/documents/information-sheets/crawlspace-insulation/
Gary
Gary