I have read a number of threads regarding annotation layers displaying oddly in the FlexViewer. This is another.
I have a Map Service which contains a lot of layers (>100), a large number of which are annotation (>15). The layers of the Map Service have been grouped into a number of logical groupings.
Having added the entire map service as an Operational Layer within App Builder the service just looks wrong. A number of annotation layers which are not by default visible are visible. It looks completely different to how it looks in the mxd. When the service is viewed via the Javascript API is looks as expected.
When normal layers are turned on/off via the LayerList widget other completely unrelated annotation layers turn themselves off/on. When annotations get turned off in this scenario red boxes get left behind where the annotation previously was.
There seems to be some relationship between the order that a layer appears within a group to which annotation layer it affects.
I have tested this in FlexViewer 3.0 and 3.1.
The underlying data is held in an FGDB having been exported from an Oracle database.
