the sc client actually makes a bad (wrong size) save file for the 2 pokemon games.. it gives you a 256kb save file when the game needs a 512kb one
you can manualy grab a 512kb sav file from the 'saver' folder where the client is installed (default path is c:/programme files/sc/saver)... just copy one and rename it to match the patched rom name
edit.. also make sure you are using the latest firmware/client 1.81/2.60