That really shouldn’t happen. Are you sure you’re in the right save folder? You should be asked to replace your old files with the new ones. Make sure the filenames are correct. The key one is called 'file1.rmmzsave'. MAKE SURE IT HAS RMMZSAVE AT THE END!
If it still doesn't work, this is sounding more and more like a problem with your PC. Have you tried playing on a different computer?