Yes, I would agree with folder ownership issue.
The permission level 644 means:
Owner: read, write
Group: read
User: read
using a script to upload the files, the owner will become the internet guest account. using FTP or another method where you log in to gain access to the folder, your account is the owner of the uploaded file. Try 666 permissions:
Owner: read, write
Group: read, write
User: read, write
This should allow you to modify files uploaded by the internet guest account. You could also have your user account added to the same group as the internet guest account then you would be able to use the 664 permisions level:
Owner: read, write
Group: read, write
User: read
