When reimaging systems they are being given the same system name. The agent is being installed fresh (using the msi) and the ePO is capturing the new Agent (with the same system name). No duplicate entries exist yet the tags manually applied to the previous system are being applied to the new agent. In some cases this is triggering unnecessary product deployments and improper policies being applied.
Are the machines being reimaged on the same hardware? If so then I would expect this to happen - ePO is seeing that the MAC address is already known, so it is associating the new machine with the existing entry in the database, including the manual tag assignments.
There's a couple of solutions: you can either make sure that the existing machine is removed from ePO before reimaging, which means ePO will treat it as a brand-new machine, or you can disable the MAC check which will also cause ePO to create a new entry for the new machine - but this means you'll have a duplicate, "orphaned" entry in ePO. For details on disabling the MAC search, please see KB57886 - it's not directly related to your issue but the solution described is the same.
I will review the KB article and find out which solution will work. Most likely it will be removing the Agent from ePO prior to reimaging.
Nope, that won't work - when the agent is reinstalled, ePO is going to see it as a new GUID with the same MAC address, and the same thing will happen again. We need to prevent ePO from associating the machine's MAC address with one already in the database, either by removing the entry, or by disabling the MAC check.