It seems that GAE expect the scenarios to be in a different place to Glest. In Glest they are all in subfolders of the same name as the scenario within the Scenarios folder. This doesn't work with GAE and crashes the program. If you move them all into the Scenarios folder itself, where GAE says it expects them, it appears to work (well at least it's loaded one but I haven't played through) but this then breaks standard Glest.
Should it not work the same as Glest with the scenarios being in the subfolders? Otherwise people are going to get confused and it requires copying (rather than moving) from every single scenario folder to get it working in both.