If all of your assembly instances are on the same configuration, they will all change to the selected part configuration. If the assembly is going to be used often, changes made by one user will affect the changes made in previous assemblies. Your best bet would be to use a design table in the assembly for the possible combinations or perhaps driveworks.
You need to set your Assembly Configurations that match the Part Configurations...
If Part A is used in 5 different Assembly Configurations then you need to have 5 different Part Configurations if they need to be different/