Again, google comes to the rescue and lets me know that the java version is not explicitly specified by default, and you could do so in the workbench.ini file by using -vm. My ini file looks a bit like this now;
--launcher.XXMaxPermSizeI was able to get this and other information from http://wiki.eclipse.org/Eclipse.ini
256m
--launcher.defaultAction
openFile
-vm
C:\Program Files\Java\jre6\bin\javaw.exe
-vmargs
-Dosgi.requiredJavaVersion=1.6
-Xms40m
-Xmx512m
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