cIOS don't have necessary USB drivers for newer HDD.
IOS58 (official IOS from nintendo) has better support for all USB commands, including "HDD wake up" command used by newer HDD, which is apparently missing from cIOS's custom and lite USB drivers.
once the drive is correctly awake and running, the console can load another IOS to continue using the drive (using read/write commands for example).
Only the Write command is having issue if you use a flash drive instead of HDD. only read command works with flashdrives, even with IOS58.