I, and many others, have had issues when using existing levels after upgrading to a newer version. It only make sense that the newer version will not display/run/execute your game made in a previous version in exactly the same way. After all, changes and enhancements were made to the engine in the way that it executes the program.
If you are working on a game that you consider important enough to finish, then I suggest you finish the game in the current engine version before upgrading the program.
Installing a previous version over 1.08 should revert the program back to it's previous state, but if not, delete the FPSC-Game.exe file from the FPS Creator directory and run the 1.04 installer again.
Best.