It's not changing the values of the existing keys.  It's changed to use completely new keys and is not taking the values for the existing ones in to account at all.
 
To make it clear for everyone.
 
From a registry export...
 
Domain level had:
"DomainMailboxesSieveLevelAdult"=dword:00000002
"DomainMailboxesSieveLevelCustom"=dword:00000002
"DomainMailboxesSieveLevelGoods"=dword:00000002
"DomainMailboxesSieveLevelHealth"=dword:00000002
"DomainMailboxesSieveLevelHoax"=dword:00000002
"DomainMailboxesSieveLevelMoney"=dword:00000002
"DomainMailboxesSieveLevelPatterns"=dword:00000002
Domain level now has:
"DomainMailboxesSieveLevel"=dword:00000002
"ScanSieveLevelCategories"=" "
It only has the later values because I forced them in there via the console.  By default they don't exist.  The upgrade process does not create them, and the default value when they don't exist is Extreme.
 
User level settings are similar, just with different key names.

Jon Benson
Mail/DNS/Linux Administrator
OzHosting.com

Just a thought, however if the install is changing the registry keys for the domain and user level anti spam settings an easy fix should be to simply backup the registry directly before the install, and then restore it directly after.  I'll have to look at

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