will the Builtin Windows Server 2008 Defragmenter disturb the optimization process run by MyDefrag?
The built-in Windows defragger only concerns itself with defragmenting files smaller than 64 megabytes. And it organizes the files that are used when booting. Other than that it leaves files alone (assuming that the disk was previously optimized with MyDefrag). So the answer is "yes", it will disturb the MyDefrag ordering somewhat, but not too much. It's useless activity, though, so I recommend turning off the built-in defragger.