Hmm, this is what I believe to be my normal Java environment:
Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.
C:\Users\jemmerling>java -version
java version "1.6.0_26"
Java(TM) SE Runtime Environment (build 1.6.0_26-b03)
Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02, mixed mode)
C:\Users\jemmerling>echo %JAVA_HOME%
C:\glassfish3\jdk
C:\Users\jemmerling>%JAVA_HOME%\bin\java -version
java version "1.6.0_26"
Java(TM) SE Runtime Environment (build 1.6.0_26-b03)
Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02, mixed mode)
C:\Users\jemmerling>
However looking at Eclipse, I can see that when Eclipse installed, it apparently found a 32-bit version of Java under C:\Program Files (x86)\Java and was able to use that. So the installation went forward with an unmodified build.xml.