When the files are uploaded they are being placed in a folder named after the node id. This is incorrect. It should instead be placing the files in a folder which is named based on the cmsPropertyData id. Uploading files manually (not using Uploadify), follows the correct pattern. If you upload a file using Uploadify then change the file associated with it, Umbraco place the new file in a different folder according to the cmsPropertyData id.

Example:

Correct:

/media/[cmsPropertyData id]/[media file name]

Incorrect:

/media/[node id]/[media file name]