Hmm! This seems peculiar to me. When you load up a matrix, they will always default to 440 and I don't know if there is a way to change the default. However, if you are using Vienna Ensemble, You should be able to save your project in whatever tuning you want. For example, due to the fact that VSL doesn't make a 2nd Violin section, I just reload the violins in another VI instance and slightly change the tuning by a cent or two. I then save my strings as a template (Save + Save Project As, etc.) When I bring the project back up, the 2nd Violins show the slightly different tuning.
Are you working in Vienna Instruments or Vienna Ensemble?