Embedded Tomcat Can't Compile JSP from JAR

I've got a problem that I can't seem to figure out. I hope someone might shed some light on this.
I have a desktop java application that has Tomcat embedded in it. I'm creating a jar file of just myapp's *.class files and I specify the main-class and classpath in the manifest file. If I execute the jar the following way, it works fine:
set CLASS_PATH=.;.\myapp.jar;.........all of the required Tomcat classes....;.\lib\anotherLib.jar
javaw -ea -classpath  %CLASS_PATH%  com.myapp.Application
But if I try to execute it this way, it runs and starts Tomcat. However, when Tomcat tries to compile a JSP, it can't find packages such as javax.servlet, javax.servlet.jsp, org.apache.jasper.runtime, and so forth.
I believe It has something to do with the classpath. Does anybody have any ideas?

i guess it is not the too lengthy classpath...
just chek that when u run the application from eclipse.. r u seting the classpath.. and that classpath should not have any spaces in it..
for ex: a directory like c:\program files \ should be as c:\progra~1\..
ot any jar file in the classpath has spaces...
this may be one of the reason that the classpath gets truncated...

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