Please check if the checkbox for auto re-write files is on....not sure if this option is available in Indigo but I remember a similar problem caused me a some trouble way back in 2009 when I was working on Eclipse 3.4 (Ganymede) with webservices plug-in for
ant 1.4 and axis 2 with an ant based compilation target! The over-write option saved the trouble of manually starting the server instance. Let me know if that helps!