ant, as seem from a command window, appears to be missing the FTP task which was working before the 10.5 install. Similarly, in Eclipse the ant task dies for want of an XML parsing class.
I had the exact sma problem! I solved it by downloading JAXP-1.4-fcs from the glasfish site and put the 2 libraries (jaxp-api.jar and jaxp-ri.jar) in Java_home/lib/endorsed. That did it. But now my Tomcat is complaining about log4j suddenly.. Well I'll get to that later..