Seems like the thing that's biting you is called DS2MB, and it's a process that copies AD settings to the IIS Metabase in a unidirectional fashion.
There's actually a subdirectory in the metabase hierarchy called DS2MB that holds all the data propagated from AD. The fact that this is happening seems to indicate that somewhere outside of IIS, something has been configured and has settings in AD that are being periodically propagated to IIS via DS2MB.
Sometimes when vdirs are screwy we deleted the DS2MB hierarchy using metabase explorer and the vdirs are automatically recreated after restarting some services (see KB883380), but in your situation, I'm guessing that the vdirs would be recreated with the settings you are trying to get rid of.
This might also be helpful for understanding what's happening:
"IIS 6.0 provides an automatic versioning and history feature by tracking changes to the configuration MetaBase file (MetaBase.xml). This file contains all the configuration settings related to IIS and can be found in the folder <Drive Name>:\Windows\system\inetsrv. Any time a change is made, the metabase history feature automatically keeps track of the changes to the metabase. When the metabase is written to disk, IIS 6.0 marks the new MetaBase.xml file with a version number and saves a copy of the file in the history folder. Each history file is marked with a unique version number, which is then available for rollback or restore. If IIS 6.0 has been running while configuration changes are being made, IIS 6.0 responds to configuration errors by automatically reverting to a previous history file, preventing errors in the configuration metabase from crashing the server."
So it's also possible that some other problem in the config is causing the system to revert back to an earlier version of the config.
Do you have Exchange Rollup 9 loaded and all the latest patches for SBS 2008? If the config problem is actually in a different part of the metabase, that might be "freezing" the metabase in one state and not letting ANY changes be made, not just the ones you are trying to make. You might try making some other minor change to the metabase and watching to see if that reverts back. If so, it would seem like it's a metabase-level problem, not a problem specific to the changes you are trying to make.
Hope this helps bring some clarity here.
Dave Shackelford
MVP
ThirdTier.net