CANON function inconsistent for modal decomposition

I have a problem with CANON functions of different Matlab versions (e.g. 2007b, 2010b, 2011a) returning inconsistent results for same call parameters: the diagonal A-matrix is OK, but the B and C matrices differ significantly. I know the modal decomposition has in multiple solutions, however, as far as I know, there is no control over the function realization. Furthermore in newer Matlab versions the canon function is a p-type and therefore inaccessible.

The obtained model is being used for tuning of predictive controller, subsequently yielding significantly different results. I have the original data generated using Matlab 2007. As I want to replicate it, and further provide public the code for performing a benchmark test, I need to have the canon function to return consistent results regardless of the matlab version used.

Is there any way to be able to get consistent modal decomposition?