Multiple file upload controls on same form via FAPI not possible? My research seems to be indicating that only a single file control widget is possible per form when creating said form with the Forms API.

Is this true? Still? 

I'm operating in D6, I don't want to use CCK because I want to keep my custom content type within a single DB table, but I do want to be able to upload multiple files - in separate form controls which lie in separate fieldsets from one another (logical context of what the file is for). 

If one uses the CCK based upload options (such as those outlined here: How to upload multiple files at once?) as soon as multiple uploads are enabled, the content type's DB table gets fragmented by having the CCK upload control's data moved to its own DB table. I don't want that. 

Is the only alternative to write some AJAX/AHAH logic handling this in the background, with the FAPI's file handling basically useless here?
I will recommend you to use:

print_r($_FILES);


This placed inside the form function submit will let you know if the files are been upload it into the temp directory and what are their names. Also check the file upload field name as sometimes when you copy and paste code you might be re-using the same name and this is creating the overwriting.

Last, but not least in your custom module try adding a single upload file field and test it if it work, then add a second and try it and so on.