The hdlsetuptoolpath command does not modify the MATLAB path; it modifies the system path, and only inside the MATLAB session that the command has been executed in, for the duration of that session. The easiest way to verify that your Xilinx install has been added to your MATLAB session's system path is to run:
>> !which ise
After you run hdlsetuptoolpath, this should return the above response. If the tool path is not set up properly, the !which system command will return nothing.
Another way to verify the path is set correctly is to examine the synthesis settings in the HDL Workflow Advisor. That tool will only show the synthesis tools that are available on the system path.