This isn't related directly to Perl, but based on this information, I agree with your guess that this is a permissions issue. In IIS, the default user name for server side programs is IUSR_{computername} and this user is configured with minimal permissions by default. You'll need to confirm that this user has the proper permissions on the directories, or change IIS to use a different user.
Comment on Re: perl 5.8.8 and windows 2000 and file writing...
The problem with that is that we use 'Windows Integrated' authentication (allows us to use %ENV to harvest logins).
However, I might see if explicitly making the IUSR_ account able to write/execute helps. You never know with Windows ! ;)