Raja,
I am not sure what your application does, but the scenario you describe is very common when trying to connect to Cortex cores while running certain applications (Linux OS included) that prevent or slow down the JTAG debugger access.
In my experience, when the application prevents the debugger from putting the Cortex core into "debug mode" there is very little that can be done apart from inserting some sort of halt mechanism at the very beginning of the code - something similar to u-boot's message that stops autoboot by hitting any key. Once the application is halted, you can connect the JTAG debugger and put the device to run again.
If your application does not power down the JTAG circuitry (some versions of the Linux kernel do that) you should be able to be connected throughout the debugging process.
Keep in mind you will have to remove this halt mechanism from the final product - which is desirable as the product and the application will not require low-level debugging anymore.
Regards,
Rafael