Resolution:
Open any .tra file (Eg; C:\tibco\tra\domain\&ltdomainname>\hawkagent_&ltdomainname>.tra), towards the end of this file I saw there is a NT service section.

# NT Service Parameters
ntservice.name=TIBHawkAgent-domain54_pcakhan-PCAKhan-00092
ntservice.displayname=TIBCO Hawk Agent (domain54_pcakhan) ntservice.starttype=automatic ntservice.binary.path.absolute=C\:/tibco/tra/domain/domain54_pcakhan/hawkagent_domain54_pcakhan.exe
ntservice.interactive=false

Take this and copy to wfjavaserver.tra; and edit it with what corresponds to WfJavaServer.

# NT Service Parameters
ntservice.name=WfJavaServer
ntservice.displayname=WfJavaServer
ntservice.starttype=manual
ntservice.binary.path.absolute=C\:/tibco/bwc/5.3/bin/wfjavaserver.exe
ntservice.interactive=false

And then register this as service:
C:\tibco\bwc\5.3\bin&gtwfjavaserver.exe --install --propFile wfjavaserver.tra