King,
You would not receive any warning, because the Core of 2008 is similar to 2003. The differences in the file system and handling make up the difference. When MR1 was released it did not support 2008.
You should definitely upgrade to MR4 MP2.
For NTP. NTP is not supported on any Server OS. You will receive in your "event viewer" Heuristic scan failures and non supported OS errors. You should consider removing this portion from the Server as it will most likely report errors that are known and may "skew" your overall reports.