Flash Exporter vs Adobe Media Exporter

Can someone explain how After Effects chooses which exporter to use for FLVs?
I have 3 different scenarios and 3 different exporters are showing up in After Effects. I would prefer to use the Flash exporter since that one seems to give us the best results.
In CS2 on my PC when I do export FLV the Flash exporter shows up.
http://www.geniusdv.com/weblog/archives/After%20Effects%20and%20Flash%20settings-thumb.gif
My co-worker just installed CS3 and when he does this option he gets the new Flash Exporter. But he can't use it because it says for him to use the render Queue. When he uses the render Queue the Adobe Media Exporter is used.
http://www.mediacollege.com/adobe/premiere/pro/export/images/vCS3_exportsettings-winmedia. gif
We do not like the results that the Adobe Media Exporter gives even when using the same settings. I never liked using in Premiere because I always had bad results and it seemed to crash a lot.
The last scenario is using CS3 on my MAC. When I do export FLV I am able to use the new Flash exporter. When going through the render queue I get the Adobe Media Exporter.
The best option would be the render queue with the Flash Exporter.
Can someone explain why there is not just one option? And why I can't set which one I want to use. We do have the Flash exporter installed on all three machines. Any help would be great!

Thanks for the reply Mylenium. I really don't want to go into the problems I am having with the encoded files. I am really just trying to understand why there are 2 separate exporters. I have done some more digging and apparently the Flash Exporter (FLV) is a quicktime exporter. Which is the one we would prefer to use. We are having errors with this exporter and sometimes it does and sometimes it doesn't work.
We are mainly having difference in encode times and quality loss when using the Adobe Media Encoder. We are exporting projects that use screen shots (which is not what AE is for.) I do notice the difference in time when exporting video projects but I have not taken the time to compare the 2 apples to apples.
Like I said I just want to understand why we are getting errors with the FLV exporter by QT.

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