ant build scripts sometimes only work from outside of netbeans -- even though its a free-form project

[emiddio-verizon]

lots of times i have to build a free-form ant project from the command line. something goes wrong if trying to build
from within netbeans. i have seen this with sun j2ee 1.4 asant projects -- which would build with just ant -- but would
not build from within netbeans - as a free form project.

most recently building apache axis-1 -- http://www.urlstructure.com/apache/ws/axis/1_4/axis-src-1_4.zip -- some of it
will build within netbeans - but all of it builds by invoking ant from the command line.

can someone explain why/how this happens -- or if there is a way to make build.xml scripts work from withing netbeans
just like they work outside of netbeans?