I'm having the same issue as gbushek and have attempted "identifyParams.layerOption = 'all';".
If I go into the mxd and turn on all the layers, the Identify operation works fine, but when I turn them all off in the mxd and then in the Flex app, use "visibleLayers" to manually turn on layers, then perform an Identify, I get no identify results. I've tried various combinations of identifyParams.layerOption and identifyParams.layerIds with no success.
Is this the intended functionality, bug or am I missing something?