It does not seem to be related to eclipse 3.5 (it has been reported with eclipse3.2 or 3.1.2).
In one case, it was because the build was using:
-Djava.endorsed.dirs
which happened to point on an old Ant version.
Another said its Ant->Runtime / "Ant Home"
was erroneously set to the current project dir.
setting it to /usr/share/ant
makes ant work properly. (But you said that "eveything was in order" there).
A third had to manually add
/usr/lib/eclipse/plugins/org.apache.ant_1.6.5/lib/ant-launcher.jar
to the Ant classpath in the preferences to make it work.
It all boils dow to an older version of Ant being somehow referenced.