Has anyone heard an update on the status of this? I think I'm having a similar issue.
We have a non-SDE SQL database that stores information on fires in a table that includes XY coordinate info. This data is updated frequently, so I'd like to have a direct link to this database that will show the most current information in my Flex app. Using an OLE DB connection and the Make Query Table tool to generate an OID, I am able to bring the table into ArcMap, create an XY event layer, and successfully publish the .mxd to ArcGIS Server. When I add the service to Flex Viewer the points appear on the map in the correct locations, but the popups all appear at XY 0,0 instead of the location where I see the point. I'm also experiencing the issue described by Kirstin if I click on a popup for a feature from a different layer first.
Exporting the event layer to a feature class in a SDE database resolves the issue, but then I lose the "live" connection to the SQL database that I wanted. I brought my map service into an ArcGIS.com map and popups work okay there - so that has me thinking that my data and service are okay. Just wondering if anyone else has dealt with this or found a workaround for this issue.