Bilal,
It is very difficult to have a precise assessment on what may be happening, especially given the reason why you are getting so many devices in the scan chain, but I can guess two things:
- A DM642 misconfiguration on the EMU pins that is causing it to start in boundary scan mode (check this thread).
- A pull up and/or down resistor that is confusing the XDS510USB but not the XDS560PCI (which typically has stronger drivers at its end). In this case, can you take a look at section 6.3 of the XDS Target Connection Guide page.
One last thing it would be trying to reduce the JTAG clock speed of the XDS510USB and see if it gives more reliable results. Check this thread for details on how to do this.
Hope this helps,
Rafael