Saving Input/Output Values and Parameters In Simulation File

Ive saved a simulation file with specific parameters and input/output values but, they dont seem to reliably save. The process here was to run a simulation from design6, setup the parameters in simulate6, then stop the simulation and save. If I run the simulation again, using the file (usually from the last used simulation), sometimes it maintains the parameters but, many times it reverts or changes on a whim. Am I missing something here or is this a bug?

The use case here is that, as our programs grow more complex there is frequently significant setup to get the program to an operating state. IE enabling estop circuits, eliminating alarms, setting inputs to reasonable operating ranges. Being able to save the simulate file with these parameters would save that setup time each time and make it easier for other users less familiar with the program (IE service or techpubs) to simulate what our end users are seeing.