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Tomcat Service VS batch file

L Peleg
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I upgrade our application from tomcat 5.5 & java 1.5 to Tomcat 6 and 1.6
When I run the tomcat 6 using batch file (using catlina.bat) it works perfectly fine, However when the tomcat is installed as service our main java script file (it is a huge Dojo resource) seems to be cut somehow and the pages are stuck with javascript errors ("Unterminated string literal".)
On same machine when I start the tomcat as batch and then run the service than everything is working fine again,
Only when I removed all installations and then install only the service it does not work again.
Any ideas?
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