When you install Waninkoko's cIOS by running cIOS38_rev14 installer, it installs it into slot 249. It also installs the same IOS into slot 250.
I think Waninkoko made it so in maxed out IOS250 when installing so Nintendo couldn't overwrite it. So, don't worry about IOS250. When you successfully install the cIOS it installs in into both 249/250 slots.
Hope that cleared some things up.
This is also why when I updated to 4.2 (officially, the day it came out) I could install cIOS38 rev14 using IOS250 without having to bugger around with other IOSes.