I just tried this in AE CS4 9.02/Flash CS4 10.0.2 and the cue points did came into Flash when exporting just the work area of a Composition in AE.
You are rendering to FLV from the Render Queue and not from File > Export, right?
Note that since FLV video uses interframe compression, some marker/cue points may not be included if they are located too close in time to the beginning or end of the work area. If you're not getting any cue points, it's probably not your case.
Thank you for the reply. Yeah, these cue points always seem selective, and we have learned about keeping the cue points a few frames away from the beginning and end. Glad to hear it works for you in the method you are using. It could be that we have Flash CS3 and AE CS4. We are definitely using the render queue. For us, through the process of elimination, it seems to only not work when the work area is shrunk down. I will try with Flash CS4 and see if there is a difference.
No problem. Let us know what you find out.