Gnucleus 1.6.1 is the latest release version, while 1.6.3 seems to be the latest beta version. go to edit/preferences and select "auto-evolve gnucleus when a beta is detected" to get the newest version. you can also download betas from
http://www.gnucleus.net/general/download.html, select "uto-Update (Manual Access)"

As for the infinite loop, it happens for me too. the new Gnucleus.exe file is downloaded to the "temp" folder, but is not replaced in the gnucleus folder. just replace the old "gnucleus.exe" file with the newer one from the temp folder, and everything works.