It's really all about appearances. If an employee leaves and then wants to come back as a contractor right away, it creates the appearance of impropriety. For example, let's say you are being audited and you tell the IRS that you cannot participate in the Audit because your computer crashed two days after receiving the audit letter. The appearance there is that you received the letter and then destroyed incriminating evidence.
The IRS does not like this one bit, and takes such maneuvers seriously. Anything that an entity or person does that seems suspicious will be assumed to be criminal, especially the "convenient" loss or destruction of evidence.