Why not browse to your SD Card and just rename the files after it's all been patched? I know it's an extra step, but if for some reason you can't change the name using the hybrid tool you certainly can rename the outputted file.
By the way, the latest loader (firmware) has built in Hybrid Mode toggle, so unless you use soft reset you don't need to use the hybrid tool if it's really giving you problems. But yeah, make sure you're using the latest hybrid tool and firmware.