[eluser]rogierb[/eluser]
Hi and welcome.
First of all be sure the path exists with is_dir() of file_exists(). If not, create it. If it gets created somewhere you don't expect it, your path is wrong.
Assuming the upload dir is in your root, use APPATH.'uploads/'.$id.'/'; for both checking and uploading.
Also, make sure the webserver is allowed to create and write the dir.