Hi Amar,
There are some related solutions about this issue in PTC support.
https://www.ptc.com/appserver/cs/view/case_solution.jsp?n=CS116543&lang=en
https://www.ptc.com/appserver/cs/view/case_solution.jsp?n=CS36748&lang=en
https://www.ptc.com/appserver/cs/view/case_solution.jsp?n=CS29628&lang=en
In our installation the problem was solved by starting the process "workerdaemon" as application instead as service and configuring the file transfer as ftp instead of network shared folder.
At this moment our big problem is to publish certain assemblyes that make Inventor 2013 to crash unexpectly while publishing from Windchill (pubblish works fine if we pubblish the same assemblyes in manual way (using publish.bat command).
Regards