This is an old thread, but I'm having a problem with this exact problem.
I have an attribute that is a file upload (an image that the customer supplies. I've added it to the product.
When I do a test order, I add a file (and yes, it's an allowable filetype) and submit the order, but there is nothing that says that the file was uploaded, and the shopping cart doesn't show that a file was attached, and the /images/uploads folder is empty.
(yes, I set the permissions to 777 and the .htaccess to allow writes)

Any more ideas?

Just one idea...
In the options Name Manaager, it says option type: File, but in the Attribute Controller the Option Value is Text. I think that's correct, as text refers to the filename, but I'm not sure.