I'll be glad to see how you will help him fix his problem with syscheck.
If syscheck report help you fix his problem, then I'm all for that too, and I would have learn something for future help I could provide to users

remember, launching gamecube only uses IOS58, not a cIOS, so the only important information you need from syscheck is a single line : IOS58
remember, if IOS58 was bad, or tempered, HBC would be upside down, Nintendont wouldn't launch at all
If the issue is really reloading to IOS58, then it's a bug in the loader and syscheck doesn't provide information about IOS58 integrity.
what I can see, which is unrelated to your issue :
slot249 is using r53 instead of r52. It's en issue only if you plug your HDD to USBPort1. if not, reinstall r52 instead, it's more stable for Wii/Wiiware game compatibility.
slot254 I thought bootmii used version 65535? but nintendo use 65280 so if you have 281 it's not the stub version.
Maybe your card is faulty or dying.
Always use "safe eject" when writing anything to the card.
Always close a program/homebrew on the console before ejecting. (close USBGX, don't eject inside USBGX)
don't put the SD card back while inside a homebrew (except HBC, which handles the SD card properly)
or maybe syscheck is really useful, and the problem is d2x r53 which has issue unmounting the SD card before reloading IOS58 to launch nintendont?
reinstall/overwrite your slot249 and test again.