Hello again Emile,
We've seen the B2E.exe thing before, but I'm not convinced it is anything to do with ETO - run your antivirus just in case.
I think this is part of what I described in my last post. By default, ETO expects to find a folder on your hard drive called Microsoft Games which contains the folder Combat Flight Simulator 3. If not, users have to take lots of care how they install ETO.
If you're getting the "MDL Patcher" title in MultiCFS3, then ETO has not been installed to a similar folder structure and MultiCFS3 has not found a valid ETO installation - as the guide tells you. This is horribly easy to get wrong if you're using a 64-bit version of XP, Vista or Windows 7 - I know, I got it wrong several times myself in Windows 7 64-bit.
As the guide tells you, you will have to delete ETO and start again. I'd strongly recommend you also delete the plain copy of CFS3.1a if it's not in Program Files\Microsoft Games\Combat Flight Simulator 3 - if you're using a 64-bit version then that will be Program Files (x86)\Microsoft Games\Combat Flight Simulator 3 - and reinstall CFS3 to the default location, patch to 3.1a and run in Quick Combat.
Then start again to install ETO. If you're using 'ordinary' Vista Home Premium (32-bit) then accept the default installation. If you're using 64-bit Vista Home Premium, follow the instructions in the Guide about paths.
Yell again if it goes belly-up!