Apache not taking jre from JAVA_HOME

I hav a wierd problem recently we moved from jre1.3 to jre 1.4
we configed all the JAVA_HOME and PATH parameters correctly.
we prepared a .bat file that looks like this:
java -Djava.endorsed.dirs="..\common\endorsed" -classpath "\bootstrap.jar" -Dcatalina.base=".." -Dcatalina.home=".." -Djava.io.tmpdir="..\temp" org.apache.catalina.startup.Bootstrap start
and put it in the server bin directory.
with this parameters the server started with jre 1.4
if we start the server from windows services with a Path to excute
D:\%TOMCAT_HOME%\bin\tomcat.exe
the server looks for the 1.3 jre installation that was there before. he fails to locate the directory and he's startup fails.
all the paramters (like JAVA_HOME) are pointing to the jre1.4 installation.
we thought the service will start with jre1.4
could any one explain why this happens and what are the steps to fix this?
the problem is the service won't start with jre 1.4

When you install Tomcat as a Service, it sets up some registry entries to keep track of things like classpath. This occurs on first installed and not when the classpath is changed.
One such entry is the JVM parameter under:
HKEY_LOCAL_MACHINE\SOFTWARE\Apache Software Foundation\Procrun 2.0\Tomcat5\Parameters\Java(on my winXP machine at least).
There may be other entries that are pertinent. Your best bet may be to re-install Tomcat to the same location so it updates the registries for you...

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