During testing, the COPASI team discovered that in some rare cases the MCA calculations display wrong results without warning the user.
The current problem with MCA calculations happens in rare cases when some reactions have extremely fast kinetics and leads to incorrect results due to numerical instabilities in the QR factorization.
This problem was introduced after version 4.11 (Build 65). One of the signs that there are problems with results is that the rows of the (scaled) Flux Control Coefficients do not add up to one. Anyone carrying out MCA calculations should check current results with those produced with version 4.11 (Build 65).
A fix to this problem is being worked on and a new version will be released as soon as possible.