The ONLY way to get into an "else" clause is for the "if" to be false. Since the "if", in this case, is
Code:
if ( (temp != "INX") && (temp != "LAX" ) && (temp != "LDX") && (temp != "DEX") && (temp != "CLX" )
the ONLY way to get into the "else" clause is for temp to equal one of those five strings. So checking when you're in the else clause is too late -- you've already done the checking, that's why you're there.

Look at your code again:
Code:
        void CLA::machinLanguageConvertor()
        {
                string temp;
                temp = commandnameptr;
                int argument = 0;


                if ( temp != "not needed" )
                {
                        argument = Atoi(offsetptr);
                        offsetptr = Oct2Bin( argument );


                        if ( (temp != "INX") && (temp != "LAX" ) && (temp != "LDX") && (temp != "DEX") && (temp != "CLX" ) )
                        {
                                CommandsBinaryString = BinaryDetector( commandnameptr );
                                CommandsBinaryString.append(mixstateptr);
                                CommandsBinaryString.append(offsetptr);

                        }

///Error .Inx wont work.

                        else
                        {
                          
                                 CommandsBinaryString = commandnameptr;
                        }
                }
                cout<<"Binary Instruction = "<<CommandsBinaryString;

        }
All the things in bright green don't happen when temp == "not needed". But yet you print out CommandsBinaryString anyway, at the bottom.