java client cant access wcf IIS Website folder

I have created a wcf webservic and hoasted it on IIS on my system.The webservice is used to upload/ download files to AppDomain.CurrentDomain.BaseDirectory (C:\FileTransfer2\IISWebsite). I was able to upload / and download file easily using .net client. But I am unable to do so using Java Eclipse. I am able to access the webservicee but then get an error saying

 javax.xml.ws.soap.SOAPFaultException: Could not find a part of the path 'C:\FileTransfer2\IISWebsite\

I am unable to understand y this folder is not accessible when being access by WCF service called by java but works works well when the service is called by .net client. Both java and .net client use the same username an are on the same machine. I have tried sharing the folder and giving my username all access.
Note that in my wcf code I use AppDomain.CurrentDomain.BaseDirectory to upload/download file which resolves to 'C:\FileTransfer2\IISWebsite\