Generally speaking, persistent variables are reinitialized if the function they are in is ever cleared, either by way of an explicit
clear TheFunctionName
or by a
clear all
There may be some situations in Simulink or SimScape that I am not familiar with in which a clear is done. (For example it would not startle me if disabling a block or subsystem had that result.)
Please check your blocks for "clear" statements. If you find any "clear all" then you should definitely remove those statements.