One problem related to manual transmission has been reported for the 2005 Mini Cooper S. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2005 Mini Cooper S based on all problems reported for the 2005 Cooper S.
24 degree morning car's manual 6-speed transmission frozen in 1st gear. Took other car to work. Problem gone after returning from work at 40 degrees. Looked up online. Saw many of the same complaints due to water in shifter cables.