Found the issue finally and fixed the problem!
Our testcases involves checking the shortcut keys which are meant for table operations such as, inserting a new row - insert key, delete a row - delete key and so on..
It seems that when swtbot executes the keystroke as,
bot.shell("").pressShortcut(Keystrokes.DELETE);
it makes the entire eclipse to hang. Am still not sure what is the reason behind it, so replaced DELETE with CTRL + Q key combination in our implementation code and then it started working fine.
Eclipse hangs even when some keystroke is added in the testcase which doesn't do any ui operations. So, did those cleanup and all the testcases are passing now :)
Seems to be a another limitation in swtbot and hope that development team will analyze this further if possible. Already have posted it in eclipse community as well. http://www.eclipse.org/forums/index.php/m/1234514/#msg_1234514
Thanks to Cpt. Senkfuss and Lula for your suggestions!!