Worspace defines a VM that doesnot contain a valid jre/lib/rt.jar - causes other issues

Worspace defines a VM that doesnot contain a valid jre/lib/rt.jar - causes
other issues

Though I found couple of related questions in StackOverflow they don't
answer my specific problem and I couldn't comment in them as I don't have
enough reputation.
I get this when I do eclipse:eclipse from Eclipse:
[WARNING] Workspace defines a VM that does not contain a valid
jre/lib/rt.jar: C:\Program Files\Java\jdk1.6.0_45\jre
JAVA_HOME: C:\Program Files\Java\jdk1.6.0_45
JRE_HOME: C:\Program Files\Java\jdk1.6.0_45\jre6
Path: %JAVA_HOME%\bin; %JRE_HOME%\bin
Also my eclipse project build path has this jre :C:\Program
Files\Java\jdk1.6.0_45\jre6
Basically I was trying to add time-out functionality to my Web-service code:
((BindingProvider)MyInterface).getRequestContext().put(BindingProviderProperties.REQUEST_TIMEOUT,
300000);
After adding this code, I added com.sun.xml.ws jaxws-rt with scope compile
in pom.xml which resulted in package not found for
com.sun.xml.internal.ws.client.BindingProviderProperties.
So i suspected the rt.jar was not loading properly. Any idea to fix the
workspace issue which I am guessing will fix the package not found issue.
Thanks.