The Site Packager seems to have an issue when you IIS 7 oder 7.5 contains an FTP Site. Once the site packager finds that site it will not let you proceed to the next step. It will tell you “Commerce Server was unable to access IIS.”
I found that it doesn’t help to stop the particular site, but you can easily comment it out in you applicationhost.config file. So you don’t loose any settings.
HTH,
Ralf
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