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CCS4: Running CPU with JTAG disconnected

I am connecting to C6472 via CCS 4.0.2, onboard XDS100USB emulation. Once I connect to a core and start running my executable, I should be able to disconnect the JTAG and let the CPU run free. Unfortunately this only works at times, say 1 out of 10. Earlier when I used to work on CCS 3.3, DM648, this was never a problem. Has this issue been fixed in the latest CCS (4.1.2), or is the fix in progress? Any concerned TI guys have a solution? Thanks in advance.