Installing JabRef on 64 bit Windows 7 with 64 bit Java (c:\program files\Java\jre6\bin) is smooth and without problems. After that whet attempting to start JabRef from short cut it says that couldn't find any JRE. When start JabRef from "c:\program files(x86)\JabRefjabref.jar" there is no problem.
Error message
I have exactly the same problem.
The problem appears to be that the shortcut points to jabref.exe. Running jabref.exe generates the can't-find-java message. Running the jar file directly does not.
-- Cem Kaner
Closed in PullRequest # 17 https://github.com/JabRef/jabref/pull/17