Render Queue FLV-flash export problem

Someone please tell me what am I doing wrong:
If I export my work to Flash Video via Render Queue, AE makes twice the file size copared to exporting it via File>Export>Flash Video(FLV).
I DO use the same exact setings of course,... and in Render Queue there is a calculation on the botom when you go and fix the settings - "size of data"/second. If I calculate that it's exactly right. But I only get that file size if I export it via File>Export>Flash Video(FLV) and not trough Render Queue.
Is that some kind of a bug in AE? What am I doing wrong??
(There is just too much work to not use the Render Queue)
I use:
Windows 64 bit
Core 2 quad
8gb ram
Adobe AE CS3 8.0.2.27
Thanks,
Met

Yes I am,... but I am doing exact same thing via File>Export>Flash Video(FLV). I am also embeding alpha there.
Like I said,... in both cases I went trough the setings (several times) just to make sure I am actualy using identical setings.
I do need the transparancy ; )
thanks
Any other suggestions??

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