Poor quality third-party save carts would corrupt my game data too, but I never had problems after switching to the official SEGA first-party carts.
The Saturn's cartridge slot was not very durable, and third-party carts have been known to cause the console's connectors to bend out of shape, causing the machine difficulty in getting a good read in the future. It's possible your Saturn got damaged by the third-party save cart and now can't always maintain a good connection to the first-party cart, leading to corrupted data. Also, this shouldn't make a difference, but you can try changing the system's battery in the back (uses the same CR2032 battery that the DC VMU's used.)