I am not sure why you are having this problem. This might be a limitation of MATLAB's daq toolbox. Can you access all 16 single-ended channels by running a test-panel in MAX? You can run a test-panel by right-clicking on the PCI-6024E in MAX within devices and interfaces select "Test Panels." If you can access all 16-channels in MAX then the PCI-6024E is working correctly; I would suggest that you contact Mathwork's support.
Is there a reason you are not using LabVIEW to interface with the PCI-6024E? LabVIEW offers a very quick and easy data acquisition solution and was built to be used with our hardware. LabVIEW also offers a multitude of built-in analysis functionality as well.
Regards,
Todd D.
Applications Engineer
National Instruments