For clarification...you get the error when following the 3.1-4.1 softmod guide right? NOT the guide in my signature?
Also, You can just Load DOP-Mii (with IOS36 v3351 on the root of your SD card) Read the warning, Press A -- Select IOS249(Should be selected already)-Press A-- Select IOS BC MIOS--- Use the D-pad to select IOS36 v3351 and Install it. It will ask you to apply patches, say YES to all.
Read the screen closely to make sure you are INSTALLING IOS36 v3351.
Edit: If that doesn't work then reinstall cIOS38 Rev 17 and try again.