OK papa; made my own little test:
Departed Honolulu Int'l (PHTO) in the 747-400, default fuel/payload, and set up the AP to put me at 10,000 indicated at 340 kts indicated, on a direct route to Hilo (PHNL).
Weather: no wind, barometer standard (29.92"), temperature at 10,000 set to freezing (0 deg. C).Don't care if any of that is realistic; it's just a test. Zero is easy to remember.
In order to steer a straight line to PHNL, the AP took up a mag heading (as confirmed by GPS and wet compass) of 110 deg. The multinav (?) display showed the same for true course (remember, VORs don't take wind and magnetic fields into account). I don't have a proper chart of that area, so I don't know the magnetic deviation there... let's assume there is none. It happens, some places.
Indicated airspeed: 340 kts.
Groundspeed as per GPS: 383 kts.
OK, it's the pressure thing, but to be sure, I break out the whiz wheel (flight computer: get one and learn to use it if you're gonna fly for real). 0 deg. C at 10,000 indicated (which, at 29.92", is close enough to exact pressure altitude for our purposes), indicated airspeed is 340... gives me a TAS of 395 kts. Twelve kts more than the GPS.
Hmmm. Not sure what's up with that, but without wind, TAS should match GS. Maybe the fudge factor I'm accepting for pressure altitude (and then there's calibrated altitude! :-/ ) is greater than I think. The good news: when I set up a GPS course back to PHTO, everything jibes, as it should with no wind... groundspeed and mag heading.
Now I add some wind: 20kts at 150 degrees, from the ground to about 13,000 ft. I reverse course again towards Hilo, and when she settles down I get:
True course (nav display):110
Mag heading (GPS, compass): 112
IAS: still 340
GS (GPS): 367
Seems logical,groundspeed reflects a quartering headwind, but lemme check with the flight computer.
TAS is still 395, wind 150 at 20 kts, squeak, scribble, etc., etc...got it!
According to the whiz wheel, with this quartering right headwind I should have:
Mag heading:112
GS:375
Again, the groundspeed is off (this time by only 8 kts), but the angles work out as they should.
Now I'll turn around and head downwind, back to Honolulu; same altitude, IAS, etc. The autopilot gives me:
True course: 290
Mag Heading: 288
Groundspeed (GPS): 398
According to flight computer:
Mag heading:288
Groundspeed: 410. Again, just like the first run with no wind, it's off by 12 knots. .And again, like the upwind leg with the quartering headwind, the angle is correct.
Bear in mind that this is a mechanical whizwheel and I didn't really sharpen the pencil first, so those groundspeeds could be off by a knot or two.Or even three...

And of course this doesn't definitively answer the question of whether or not there's innacuracy in indicated altitude at standard pressure or GPS groundspeed in FS9, but it may put to rest your concerns about your own install. However, if you're really seeing two different groundspeeds along the same course line with no wind (are you absolutely sure it was set at zero knots?), I don't know what to tell you...
If anybody has an electronic flight computer, I'd like to see results of a similar test done with that (more precise)...
A flight computer does all the number-crunching for you: even a mechanical whiz-wheel (basically a multifunction circular sliderule) does the job nicely if more slowly than an electronic one, and requires no batteries. They're used not only for planning, but for finding unknown data in flight, as well. Very handy.