Hammer Program messed up?

Alright. Two weeks ago, Hammer was working fine. Now, whenever I make a map, hammer (or something) wants to go and create another folder named "program". It seems as if it thinks that this is the folder with all the info, and it goes off of that.
(Directory Structure: C:/program)
(Valve Structure: C:/program files/valve/...)
Also, it gives me the lights.rad error, I even put the lights.rad file into the vrad.exe folder. I know it has to be the program, because all my maps created/compiled for it are messed up. (I did the SDK release notes tutorial letter for letter and it still gave me errors) So, if anyone can help.

I'm using the included skybox tutorial.
Here is the compile messages:

** Executing...
** Command: "c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk\bin\vbsp.exe"
** Parameters: -game "c:\program files\valve\steam\steamapps\shadowsoze\counter-strike source\cstrike" "C:\Program Files\Valve\Steam\SteamApps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox"

Valve Software - vbsp.exe (Jan 19 2005)
2 threads
materialPath: c:\program files\valve\steam\steamapps\shadowsoze\counter-strike source\cstrike\materials
Loading C:\Program Files\Valve\Steam\SteamApps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox.vmf
fixing up env_cubemap materials on brush sides...
ProcessBlock_Thread: 0...1...2...3...4...5...6...7...8...9...10 (0)
ProcessBlock_Thread: 0...1...2...3...4...5...6...7...8...9...10 (0)
Processing areas...done (0)
Building Faces...done (0)
Chop Details...done (0)
Find Visible Detail Sides...
Merged 6 detail faces...done (0)
Merging details...done (0)
FixTjuncs...
PruneNodes...
WriteBSP...
done (0)
writing C:\Program Files\Valve\Steam\SteamApps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox.prt...done (0)
Creating default cubemaps for env_cubemap using skybox sky_dust...
Run buildcubemaps in the engine to get the correct cube maps.
Finding displacement neighbors...
Finding lightmap sample positions...
Displacement Alpha : 0...1...2...3...4...5...6...7...8...9...10
Building Physics collision data...
done (0) (13390 bytes)
Emitting linux collision data (use -nolinuxdata to disable).
Building Physics collision data...
done (0) (13390 bytes)
Placing detail props : 0...1...2...3...4...5...6...7...8...9...10
Writing C:\Program Files\Valve\Steam\SteamApps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox.bsp
1 second elapsed
Memory leak: mempool blocks left in memory: 49
Memory leak: mempool blocks left in memory: 1

** Executing...
** Command: "c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk\bin\vvis.exe"
** Parameters: -game "c:\program files\valve\steam\steamapps\shadowsoze\counter-strike source\cstrike" "C:\Program Files\Valve\Steam\SteamApps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox"

Valve Software - vvis.exe (Dec 15 2004)
2 threads
reading c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox.bsp
reading c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox.prt
5 portalclusters
4 numportals
BasePortalVis: 0...1...2...3...4...5...6...7...8...9...10 (0)
PortalFlow: 0...1...2...3...4...5...6...7...8...9...10 (1)
Optimized: 0 visible clusters (0.00
Total clusters visible: 17
Average clusters visible: 3
Building PAS...
Average clusters audible: 3
visdatasize:54 compressed from 80
writing c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox.bsp
1 second elapsed

** Executing...
** Command: "c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk\bin\vrad.exe"
** Parameters: -game "c:\program files\valve\steam\steamapps\shadowsoze\counter-strike source\cstrike" "C:\Program Files\Valve\Steam\SteamApps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox"

Valve Software - vrad.exe (Jan 18 2005)
----- Radiosity Simulator ----
2 threads
Could not find lights.rad in lights.rad.
Trying VRAD BIN directory instead...
[Reading texlights from 'c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk\bin\lights.rad']
[1 texlights parsed from 'c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk\bin\lights.rad']

Loading c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox.bsp
89 faces
43605 square feet [6279239.00 square inches]
0 displacements
0 square feet [0.00 square inches]
89 patches before subdivision
409 patches after subdivision
3 direct lights
BuildFacelights: 0...1...2...3...4...5...6...7...8...9...10 (2)
BuildVisLeafs: 0...1...2...3...4...5...6...7...8...9...10 (0)
transfers 7989, max 104
transfer lists: 0.1 megs
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #1 added RGB(4932, 3754, 1850)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #2 added RGB(559, 265, 100)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #3 added RGB(69, 24, 6)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (1)
Bounce #4 added RGB(9, 2, 0)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #5 added RGB(1, 0, 0)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #6 added RGB(0, 0, 0)
Build Patch/Sample Hash Table(s).....Done<0.0011 sec>
FinalLightFace: 0...1...2...3...4...5...6...7...8...9...10 (0)
FinalLightFace Done
Ready to Finish
0 of 0 (0% of) surface lights went in leaf ambient cubes.
ComputePerLeafAmbientLighting: 0...1...2...3...4...5...6...7...8...9...10

Object names Objects/Maxobjs Memory / Maxmem Fullness
------------ --------------- --------------- --------
models 1/1024 48/49152 ( 0.1
brushes 35/8192 420/98304 ( 0.4
brushsides 273/65536 2184/524288 ( 0.4
planes 264/65536 5280/1310720 ( 0.4
vertexes 195/65536 2340/786432 ( 0.3
nodes 33/65536 1056/2097152 ( 0.1
texinfos 91/12288 6552/884736 ( 0.7
texdata 18/2048 576/65536 ( 0.9
dispinfos 0/0 0/0 ( 0.0
disp_verts 0/0 0/0 ( 0.0
disp_tris 0/0 0/0 ( 0.0
disp_lmsamples 0/0 0/0 ( 0.0
faces 89/65536 4984/3670016 ( 0.1
origfaces 66/65536 3696/3670016 ( 0.1
leaves 35/65536 1960/3670016 ( 0.1
leaffaces 89/65536 178/131072 ( 0.1
leafbrushes 61/65536 122/131072 ( 0.1
surfedges 649/512000 2596/2048000 ( 0.1
edges 433/256000 1732/1024000 ( 0.2
worldlights 2/8192 176/720896 ( 0.0
waterstrips 2/32768 20/327680 ( 0.0
waterverts 0/65536 0/786432 ( 0.0
waterindices 21/65536 42/131072 ( 0.0
cubemapsamples 2/1024 32/16384 ( 0.2
overlays 0/512 0/180224 ( 0.0
lightdata [variable] 17120/0 ( 0.0
visdata [variable] 54/16777216 ( 0.0
entdata [variable] 798/393216 ( 0.2
occluders 0/0 0/0 ( 0.0
occluder polygons 0/0 0/0 ( 0.0
occluder vert ind 0/0 0/0 ( 0.0
detail props [variable] 1/12 ( 8.3
static props [variable] 1/202 ( 0.5
pakfile [variable] 9906/0 ( 0.0

Win32 Specific Data:
physics [variable] 13390/4194304 ( 0.3

Total Win32 BSP file data space used: 75264 bytes

Linux Specific Data:
physicssurface [variable] 13390/6291456 ( 0.2

Total Linux BSP file data space used: 75264 bytes

Total triangle count: 205
Writing c:\program files\valve\steam\steamapps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox.bsp
3 seconds elapsed

** Executing...
** Command: Copy File
** Parameters: "C:\Program Files\Valve\Steam\SteamApps\shadowsoze\sourcesdk_content\cstrike\mapsrc\sdk_3d_skybox.bsp" "c:\program files\valve\steam\steamapps\shadowsoze\counter-strike source\cstrike\maps\sdk_3d_skybox.bsp"

** Executing...
** Command: "c:\program files\valve\steam\steamapps\shadowsoze\counter-strike source\hl2.ex

Try resetting the game configurations in the SDK menu, then refresh SDk content.

Considering this was posted on Jan 30th, I think Shadow has left this forum considering that he only has 1 snarkmark, and it not coming back. Even if he were still here, he would have figured it out or moved on by now. Especially with the many updates since Jan. 30th.