According to Help Fixer and my own review the compareTo() method in com/mcjty/rftools/commands/DefaultCommand.java is invalid and as such will randomly break help.

Solution below, I still don't know how to do a proper PR or I would...

@OverRide
public int compareTo(Object o) {
return 0;
}

to

@OverRide
public int compareTo(Object o) {
return getCommandName().compareTo(((ICommand)o).getCommandName());
}

Fixed in next release.