Well, actually, if you consider what you're doing, TestComplete is doing exactly what it needs to do. When the project is run, it updates a number of files and then does a "save". Well, the date on the files is compared to the system date to determine if any of the files have changed. It sees a difference and reports it.
In other words, I don't think there is an easy way to "fix" this.
A question: What is your goal in changing the system date in script code? What are you trying to test? Is there some other way of testing the same thing without manipulating the system date?
I am trying to test how some databases are managing records over a span of 2 years and specially under Daylight Saving Time changes. Sometimes, DST will advance 1 hour, sometimes it will just go back in time for 1 hour.