I recall we have a problem with 9.3 ArcGIS Servers. Try setting the scale dependency on each layer, not on a group layer. This should solve your problem.
We're having trouble accessing your server right now. It could be down. Queries against the particular service don't seem to work. How is your service configured? Have you enabled security on it?
Yes, our server was having issues late last week. Those have been resolved. I also removed all group layers to see if this would fix the issue. It has not. The service is configured on ArcGIS Server 9.3 as a pooled map service. No security exists except for a firewall. The updated path is http://www.arcgis.com/home/webmap/viewer.html?webmap=fa9b8cf1c58142da93d52f68b74850c4
The queries ArcGIS.com sends to your server are failing. I did a little more investigating and found this forum post that discusses the particular error I'm seeing ("Unable to perform query. Please check your parameters").
There is a reference to SP1 having a fix for the problem. Based on the date of the forum posts, that would appear to be 9.3 SP1. You can find the download here.
We'll have to take a look. Can you share the URL to your map? Also, are you running the ipad application or just using the Safari browser? I think you're using the app. You might try simply using the browser too...
