Did a System Restore and got to a point where Mobipocket actually used to work, now I just got some odd folders from some days ago I need to take care off and other stuff but Mobipocket is atleast up and running again.
I've started having the same problem today where the screen pops up like that, simply really distorted, showing a few images and other stuff but non useable. Did the same thing as you, installed, uninstalled, installed, tried different folders (default and custom ones), different versions, different modules and cleaned registry of it a couple of times. Everything is clean, new install, same problem.
To my happiness I came across this guide, went on treasure hunt in regedit, to much dismay: No such 'parasite zone' in named path...
Been running smoothly up til now. Did move the folder containing the program before it happened though from C:/Users/Robert/Documents/Kindle Converters/Mobipocket to XXX/Documents/Kindle Related/Kindle Converters/Mobipocket. Have changed folder that way before though without issues (New computer, still rearranging stuff everyday) which only resulted in me having to update my Mobipocket desktop shortcut.
Any ideas? I'm using a Win 7 Home Premium Acer with x64 processor by the way.