Same here, the good news is I have a workaround.
Create a batch file in the game directory comtaining the following:
taskkill /f /IM explorer.exe
Empires2.exe
start explorer.exe
Run the batch file and enjoy the fixed graphics. If you're on XP you may not have 'taskkill' (test first, before launching the script). If that's so you can download it here (not my site, may be useful): http://members.ziggo.nl/gigajosh/2005/05/taskkillexe.html
I've read that the problem occurs with many display management style applications, not just Fences, and may be related to the way that Vista / Win7 force the taskbar to the front all the time. That doesn't explain why the same thing occurs in XP, though. I've seen it with many older games, including educational games my children play.
With this fix you don't need any compatability modes setting for AoE2, and I've verified that the 'taskkill' approach works with XP Home and Win7 Home Premium.
I've posted this previously and received a response from Stardock support, but it's not percieved as a Fences bug so don't expect a fix. Technically that might be true, but it doesn't happen without Fences (on XP), does happen with, and I'd have thought a workaround could be achieved by those clever Stardock folks. Lets hope for the best.
Let me know if this works for you, or if you need more of a walkthrough around setting up batch files and suchlike.