Issues with file permissions when migrating site between servers

Hi all,
I'm having difficulty migrating a site between windows servers. They are both Win2k3 running IIS6. I'm also running the Ionics Isapi Rewrite tool.
I can get the site migrated fine and up and working on the new server. From a site visitor perspective, it's all good.
From an admin perspective though, I'm having big issues with the permissions on files that have been added.
When removed from Drupal (6), the files are removed from the page, but not deleted from the file system. If I add a new file and remove it, then it works as expected, so something (or some permission) has been lost in the FTP transfer of the site.
I have tried adding IUSR to the files folder to ensure that that permission exists. I have also changed the Owner of all the files to IUSR, but this doesn't help either.
I'm hoping there is something simple that I'm missing. When comparing permissions between a newly added file and one that has been transferred over, there doesn't seem to be any difference.
Any ideas? I'm running out.
Thanks.