I'll assume your JAR contains a section similar to this:
Classpath: lib\axis.jar
lib\axis-ant.jar
This is a single value split onto multiple lines (the first line, and a continuation line). It is exactly equivalent to:
Classpath: lib\axis.jarlib\axis-ant.jar
The newline and space that indicates a continuation line is not part of the value.
The value needs to include a space between the two filenames. For example (still using a continuation; note the extra space):
Classpath: lib\axis.jar
lib\axis-ant.jar
Also, note that the JAR tool is within its rights to adjust how lines are split, since this doesn't affect how the value is interpreted. This:
Classpath: lib\axis.j
arlib\axis-ant.jar
is still equivalent to:
Classpath: lib\axis.jarlib\axis-ant.jar
so the JAR tool is not doing anything wrong by making that change.