No, no...
What I said in my first post holds true. WINDS DON'T MATTER, GS will ALWAYS ALWAYS be higher than KIAS when you're in the air.
It's just the way the world works.
This isn't going to help papa with his problem, but that statement is false. If you're showing, say, 100kts on your airspeed indicator, and you're flying within a mass of air that is moving in the opposite direction over the ground at a speed of 10kts relative to the ground, your speed along your course- your groundspeed- will be 90 kts. That will be confirmed by GPS, by observers on the ground, whatever you like.
Likewise, if you are moving at 100kts IAS in the same direction as that mass of air ("wind"), say, on your way home, and that wind is blowing at 10 kts, your groundspeed will be 110 kts. If the wind is not aligned precisely with your course, it won't precisely equal the sum of or difference between your airspeed and the wind speed, but you get the idea...it's just like being in a rowboat on a river. You're rowing upstream towards your destination, and making good progress despite the current.. Drop the oars and what happens? You start to slow down (relative to the shoreline). Wait a sec, and you'll start going backwards! Turn your boat around, and without any rowing at all, you'll still be moving forwards (just going the other way). Add power (rowing) and now you're really moving! If you substitute plane and wind for boat and current, you see it's the same situation.
It is even possible to fly backwards along your intended course- at a negative groundspeed, so to speak- if your airplane is slow and the winds are strong.
As for papa's problem, it seems to me like a problem with part of the sim program itself. You shouldn't always have a tailwind... my experience in real life and many stories told to me by other pilots have led me to always assume that the time you save with a tailwind on the way out on a round trip will almost always be taken away from you on the way back, unless there's a major weather change over a large area, like a passing front. A tailwind on both legs of a round-trip is so rare as to be considered practically impossible!
Then there's the fact that you set the winds for zero...
As for crosswinds, they almost always factor in as headwinds. What I mean is: even if the wind is square to your course, you'll probably see a reduction in groundspeed. The precise reason for that is best explained by an aeronautical engineer, not me...
I can't confidently suggest a fix, papa: you should at least check for this anomaly with other aircraft. Maybe you need to fiix your 747 files, or...?
Hey, did you hit Shift+ Z to show altitude, heading, and winds? Try it if you didn't. If you see windspeed indicated there, despite setting no wind in your weather scheme, then there's definitely something screwy!
I am flying the default 747-400 from Chicago Ohare to Toronto using realistic settings and weather. I have tried changing weather but still get the same effect no matter what settings I use. My last download was PAI installer with Mesaba and American Eagle and the Airbus 380 with new United Airlines textures (from this site FS2004 Civil Aircraft page 93). No other changes have been made to the system. I have tried the Airbus and it is affected as well. 
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