Resolution: Open any .tra file (Eg; C:\tibco\tra\domain\<domainname>\hawkagent_<domainname>.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>wfjavaserver.exe --install --propFile wfjavaserver.tra