I have used secured a service in AGS manager, and then generated 300 day token via the token manager at the rest end point. I have tested that token in the JavaScript API (scandelouse aren't I...). The token and maps seems to work in my basic JS map, so I'm pretty sure that is good. I have placed this jsmap in the same folder as my flex index.html file, so they are running from the sample place, since the token is tied to that url, per the token generating screen.
I have then added my token to my config file as so:
The I then dump the cache in the browser and load the Flexviewer. No errors occur in the viewer, and the "More..." button in the viewer displays the name of my service by no data layers underneath it.
Via Fiddler I'm seeing an error: POST /ArcGIS/rest/services/MyProject/MyService/MapServer/query?token=gVxKVHcjS%5FywXHS7ymQJnEfmq04sfOvFF2ntWUiWPKxW%2DeAxUJ%2D9osTofc6kP9ZmM8cugZ9QRadK%2DSqRs29%5F3g%2E%2E
[h=2]Error [h=3]Specified format is not supported Code: 400