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I use Clean as first option and delete as the second one. Why would you want to keep infected files that are infected. If its a legit program that's infected you'll have to reinstall it anyway.
I agree with Turift. The default setting for ODS is to 1)Clean and then 2) delete the files. I can't think of a good reason why this setting would be changed to anything else.
Also, you must remember that not all files can be dealt with right away. Often times Virus scan must wait until it has full access to a file before it can clean/delete it. This full access occurs once a reboot has occurred. After the reboot, Virus Scan will deal with the infected file before any other services get attached to it.
Hope that helps!