IIRC, we abandoned the practice of Zope running as System Account in favor of running as a specific user "zope", because we would have had to give System Account extra privileges to access remote file systems and ODBC connections. That would have been a security flaw (hacking Zope's machine would give you access to the remote resources as well).
I try to avoid getting into that since Windows permissions drive me nuts after a while. We have an isolated web cluster, so hacking into one Zope as the System Account will only give you access to 2 other Zope boxes. All the fun stuff is in a seperate domain. As anymore issues on that I couldnt tell you... I let the sys admins handle that, and they said running as that is fine so I let them worry about it.
This'll be good fodder for your Zope-on-Windows FAQ/HowTo. How that going?
Its on my list of things to do... yes, if I could just work on zope all day long I might get to it one day :) Cheers. -- Andy McKay.