They must be using a different ircd... the freenode docs say that the command should be in the format: /mode <+/-> with valid options
+i +g +w +D +Q +R +Z
e.g., /mode Colani600 +R
So ... maybe the issue is that Grapevine and Chatbox are just issuing "/mode colani" without any parameters - is there a setting in the app to customise log on mode parameters? You could add +R, or set /umode Colani600 +i
Or maybe it's trying to set a channel mode that has parameters incorrectly ... but why would it do that?