OK - looking at that I can see where it is failing. I can see it is going down a path that is specific to the case where you are using 64-bit Java and do not have the JAVA_HOME environment variable set. I suspect it is a quoting problem somewhere (although I cannot yet see why!). It is also not clear why others running 64-bit Java on Windows are not seeing the same problem (unless they are and have not yet reported it). The strange thing is I did not think that specific path had changed from the 3.0 release although it must have I guess.
My suggestion is that as a temporary fix you insert lines at the top of the rungui.cmd file that read
START "Calibre2Opds" "C:\Program Files (x86)\Java\jre6" -Xms128m -Xmx512m -cp OpdsOutput-3.1-SNAPSHOT.jar Gui
That will supersed the rest of the file that tries to derive the correct parameters for your system by hard-coding them.
I will see if I can pin down the problem, and then give you an updated rungui.cmd file so you can check I have got the fix right for future releases. I do not have a 64-bit sytem of my own so have to rely on others reporting and testing issues that they throw up.