Just as a test, try loading one of the default scenarios, changing something obvious (like moving a vessel), quicksaving, quitting, and then reloading from the quicksave. If that works, then the problem is most likely with some addon vessel you're using in that scenario. If that fails, try it again after disabling everything in the Modules tab. If that fails, try making a new orbiter installation (a "clean" one, to use the common terminology), and before doing anything at all with it, try the load, change, quicksave, quit, load sequence with it. If that fails, there's something wrong with your computer, or there's some sort of fundamental misunderstanding between me, you and the manual, and I have no idea what that might be.

BEGIN_DESC
The Ares lander in a dock in Mars orbit.
Keys:
C .. Chute deploy and chute cut
J ... Jettison heat shield; jettison gear before takeoff
END_DESC
BEGIN_ENVIRONMENT
System Sol
Date MJD 66478.0072874768
END_ENVIRONMENT
BEGIN_FOCUS
Ship Ares
END_FOCUS
BEGIN_CAMERA
TARGET Ares
MODE Extern
POS 4.00 21.46 -65.78
TRACKMODE TargetRelative
FOV 50.00
END_CAMERA
BEGIN_HUD
TYPE Docking
END_HUD
BEGIN_MFD Left
TYPE Map
REF Mars
END_MFD
BEGIN_MFD Right
TYPE Docking
TARGET Dock
END_MFD
BEGIN_SHIPS
ISS:ProjectAlpha_ISS
STATUS Orbiting Earth
RPOS -6396454.47 2014857.52 670746.25
RVEL 1974.160 7041.767 -2369.949
AROT 110.00 -10.00 80.00
PRPLEVEL 0:1.000
IDS 0:588 100 1:586 100 2:584 100 3:582 100 4:580 100
NAVFREQ 0 0
XPDR 466
END
Dock:P_Ares-dock
STATUS Orbiting Mars
RPOS 2951324.58 0.74 -2044154.26
RVEL -1966.615 0.011 -2838.719
AROT -0.57 1.52 -105.69
RCSMODE 2
DOCKINFO 0:0,Ares
IDS 0:20 100
NAVFREQ 0 0
XPDR 466
END
Ares:P_Ares
STATUS Orbiting Mars
RPOS 2951324.61 0.75 -2044155.34
RVEL -1966.615 0.011 -2838.719
AROT -0.57 1.52 164.31
RCSMODE 2
PRPLEVEL 0:1
DOCKINFO 0:0,Dock
NAVFREQ 20 0
XPDR 468
MODE 0
END
END_SHIPS
(remove the dots)
It is in the same folder as the Doc folder, the scenario folder, all other folders and the orbiter.exe.
It is the same directory where you double click the orbiter.exe to run it.
If you have Vista and haven't turned off UAC, you'll need to click the "compatibility files" button near the top of the Windows Explorer window to find it.
UAC:Whats the UAC and how do u do that (more detailed).
**** Orbiter.log
Build Sep 29 2006 [v.060929]
Devices enumerated: 6
Devices accepted: 5
==> RGB Emulation
==> Direct3D HAL
==> Direct3D T&L HAL
==> Direct3D HAL (NVIDIA GeForce 7150M / nForce 630M)
==> Direct3D T&L HAL (NVIDIA GeForce 7150M / nForce 630M)
Found 0 joystick(s)
Module AtlantisConfig.dll [API v.060425]
Module DGConfig.dll [API v.060425]
Module EnergyConfigurator.dll [API v.060425]
It's not inside a folder inside the root folder, it's in the root folder. UAC is only in Vista, and I believe enabled by default. It stands for something like User Access Control, and is used to provide more security for a multi user OS.