Multiple file upload controls on same form via FAPI not possible?
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.