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When I start encoding, there is only the black dos window opening for a very short time when I use your gui.
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Well, I guess the GUI needs some instructions. You have to place both avs2avi.exe and mencoder.exe in the same directory as the GUI itself. Try that and if it doesn't work, start a command prompt (start - run - type "cmd" without the "s and press OK,= then navigate to the directory you have put the gui - for instance c:\temp\x264gui\, and then run jobs.bat. If it also aborts immediately, please post the contents of your dos window here.
Also, you need a very recent mencoder version from celtic-druid, not the version you can download from the mplayer homepage.