Suggest RGBA UtVideo FourCC="ULRA" or pretty much any RGB32 codec.
I've no idea who AFX users are or how they encode logo (most people here want to get rid of logos, not create them).
VirtualDub might be better suited to writing logos then Avisynth, but could use avisynth Overlay with mask.
One of the previous versions of your post has several scripts, few people here are clairvoyant, where you use someone else's script, then
best post a link or script itself, I googled for the said scripts and found nothing.
Also, maybe try Search (top of this web page) for 'Logo' in 'Avisynth Usage' and 'VirtualDub' forums.
EDIT:
Overlay:
http://avisynth.nl/index.php/Overlay
Layer:
http://avisynth.nl/index.php/Layer
EDIT: Note this from Overlay Docs
Quote:
Using RGB32 alpha channel
Overlay will never use the alpha channel given in an RGB32 clip. If you want to extract the alpha channel from an RGB32 clip you can use the ShowAlpha command to extract the alpha information. For maintaining maximum quality it is recommended to extract the alpha as RGB.
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