Can you please attach the model as it will be difficult to conclude anything without that.
However, one reason for this may be the way variant conditions are resolved. The resolution of variant conditions is done in the closest context i.e if same variables are defined in base, model and mask workspace then mask worksapce is preferred followed by model workspace and then base worksapce.
Kindly refer to the following documentation link for better understanding of storage locations of variant control variables: https://www.mathworks.com/help/simulink/var/variant-control-modes-in-variant-blocks.html#mw_3507ce0d-5290-4879-8778-71ae84dcc129
