Please submit the sample which you think McAfee falsely detected as described here:
Generally speaking, McAfee will clean silently if that's how your product is configured. If you want to be prompted, you need to configure UserPromt as a default cleaning action.
Even though, you should be able to see the record of the supposed infection in VirusScan log. If there is none, then it's likely that your program disappearance has nothing to do with McAfee.
Hope that helps,