This issue is caused by the mechanism EPO uses when an AD Sync task moves a machine from one location in the EPO system tree to another (I assume you have your AD Sync task set to Move systems from their current System Tree location to the synchronized group). It does not actually "move" the active entry rather it deletes the active entry and creates a new blank entry in the new group thus stripping all the tags.
I certainly understand how this functionality may cause you some grief. As this is how EPO is designed you should submit a Feature Modification Request (FMR) explaining why this is causing you difficulty and suggest an alternate method. An example of an alternate method would be to have the AD Sync task move the active entry to the new group rather than deleting the active entry and creating a blank one in the new group.
You can submit FMRs here: