Is it okay to use this cIOS for games?
For games, if some don't work, you can change the CIOS for each game in your game settings before launching them. You can set it to CIOS 249, 250, or 248.
For example, Just Dance and Call of Duty use CIOS 250 with base 57.
cIOS numbers mean nothing, what matters is what custom IOS is installed on that slot ("container number") and what base IOS where used
There is a guide of recommended ones. Are you following the guide?
ModMii recommends using this cIOS on this Slots
Slot 248, IOS base 38, d2x v11-beta1
Slot 249, IOS base 56, d2x v11-beta1
Slot 250, IOS base 57, d2x v11-beta1
slot 251, IOS base 58, d2x v11-beta1
On my notes I have this explanation:
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Slot 248 base 38: only bases 38 & 58 can play SpongeBob's Boating Bash, and only 38 has USB keyboard support for Animal Crossing
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Slot 249 base 56: plays majority of games and a few that base 57 cannot; preferred for slot 249 to avoid unnecessary IOS reloads under USB Loader GX's Auto IOS setting
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Slot 250 base 57: plays majority of games and a few that base 56 cannot
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Slot 251 base 58: only bases 38 & 58 can play SpongeBob's Boating Bash, and only 58 supports the LAN adapter