I tried searching, but there are just so many threads on water problems
that I couldn't refine the search enough to find a solution. A
couple times it was brought up but no one seemed to know what to do.
Here are two shots of the problem in action:

And here's my compile log:
** Executing...
** Command: "C:\Program Files\Valve\Steam\SteamApps\kerosine99@aol.com\sourcesdk\bin\vbsp.exe"
** Parameters: -game "C:\Program
Files\Valve\Steam\SteamApps\kerosine99@aol.com\half-life 2
deathmatch\hl2mp" "C:\Documents and Settings\Thomas
Boardman\Desktop\mymaps\prefuncdetail"
Valve Software - vbsp.exe (Jan 19 2005)
1 threads
materialPath: C:\Program
Files\Valve\Steam\SteamApps\kerosine99@aol.com\half-life 2 deathmatch\hl2mp\materials
Loading C:\Documents and Settings\Thomas Boardman\Desktop\mymaps\prefuncdetail.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 60 detail faces...done (0)
Merging details...done (0)
FixTjuncs...
PruneNodes...
WriteBSP...
done (0)
writing C:\Documents and Settings\Thomas Boardman\Desktop\mymaps\prefuncdetail.prt...done (0)
Creating default cubemaps for env_cubemap using skybox sky_wasteland02...
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) (109829 bytes)
Emitting linux collision data (use -nolinuxdata to disable).
Building Physics collision data...
done (0) (167162 bytes)
Placing detail props : 0...1...2...3...4...5...6...7...8...9...10
Writing C:\Documents and Settings\Thomas Boardman\Desktop\mymaps\prefuncdetail.bsp
5 seconds elapsed
Memory leak: mempool blocks left in memory: 48
Memory leak: mempool blocks left in memory: 5
** Executing...
** Command: "C:\Program Files\Valve\Steam\SteamApps\kerosine99@aol.com\sourcesdk\bin\vvis.exe"
** Parameters: -game "C:\Program
Files\Valve\Steam\SteamApps\kerosine99@aol.com\half-life 2
deathmatch\hl2mp" "C:\Documents and Settings\Thomas
Boardman\Desktop\mymaps\prefuncdetail"
Valve Software - vvis.exe (Dec 15 2004)
1 threads
reading c:\documents and settings\thomas boardman\desktop\mymaps\prefuncdetail.bsp
reading c:\documents and settings\thomas boardman\desktop\mymaps\prefuncdetail.prt
80 portalclusters
189 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 (0)
Optimized: 24 visible clusters (0.00%)
Total clusters visible: 3352
Average clusters visible: 41
Building PAS...
Average clusters audible: 72
visdatasize:2258 compressed from 2560
writing c:\documents and settings\thomas boardman\desktop\mymaps\prefuncdetail.bsp
1 second elapsed
** Executing...
** Command: "C:\Program Files\Valve\Steam\SteamApps\kerosine99@aol.com\sourcesdk\bin\vrad.exe"
** Parameters: -game "C:\Program
Files\Valve\Steam\SteamApps\kerosine99@aol.com\half-life 2
deathmatch\hl2mp" "C:\Documents and Settings\Thomas
Boardman\Desktop\mymaps\prefuncdetail"
Valve Software - vrad.exe (Mar 8 2005)
----- Radiosity Simulator ----
1 threads
[Reading texlights from 'lights.rad']
[45 texlights parsed from 'lights.rad']
Loading c:\documents and settings\thomas boardman\desktop\mymaps\prefuncdetail.bsp
641 faces
30925 square feet [4453277.00 square inches]
3 displacements
153 square feet [22062.13 square inches]
641 patches before subdivision
3849 patches after subdivision
16 direct lights
BuildFacelights: 0...1...2...3...4...5...6...7...8...9...10 (4)
BuildVisLeafs: 0...1...2...3...4...5...6...7...8...9...10 (4)
transfers 208507, max 216
transfer lists: 1.6 megs
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #1 added RGB(12188, 11359, 5201)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #2 added RGB(2305, 2020, 777)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #3 added RGB(483, 398, 130)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #4 added RGB(96, 74, 21)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #5 added RGB(21, 16, 4)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #6 added RGB(4, 3, 1)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (1)
Bounce #7 added RGB(1, 1, 0)
GatherLight: 0...1...2...3...4...5...6...7...8...9...10 (0)
Bounce #8 added RGB(0, 0, 0)
Build Patch/Sample Hash Table(s).....Done<0.0082 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
237/8192
2844/98304 ( 2.9%)
brushsides
1694/65536 13552/524288
( 2.6%)
planes
790/65536 15800/1310720 (
1.2%)
vertexes
1079/65536 12948/786432
( 1.6%)
nodes
284/65536 9088/2097152
( 0.4%)
texinfos
89/12288
6408/884736 ( 0.7%)
texdata
33/2048
1056/65536 ( 1.6%)
dispinfos
3/0
528/0 ( 0.0%)
disp_verts
243/0
4860/0 ( 0.0%)
disp_tris
384/0
768/0 ( 0.0%)
disp_lmsamples
460/0
460/0 ( 0.0%)
faces
641/65536 35896/3670016 (
1.0%)
origfaces
522/65536 29232/3670016 (
0.8%)
leaves
286/65536 16016/3670016 (
0.4%)
leaffaces
710/65536
1420/131072 ( 1.1%)
leafbrushes
529/65536
1058/131072 ( 0.8%)
surfedges
5072/512000 20288/2048000 ( 1.0%)
edges
3009/256000 12036/1024000 ( 1.2%)
worldlights
16/8192
1408/720896 ( 0.2%)
waterstrips
35/32768
350/327680 ( 0.1%)
waterverts
0/65536
0/786432 ( 0.0%)
waterindices
609/65536
1218/131072 ( 0.9%)
cubemapsamples
3/1024
48/16384 ( 0.3%)
overlays
1/512
352/180224 ( 0.2%)
lightdata
[variable]
298388/0 ( 0.0%)
visdata
[variable] 2258/16777216 (
0.0%)
entdata
[variable] 14248/393216
( 3.6%)
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]
1/2566 ( 0.0%)
pakfile
[variable]
43062/0 ( 0.0%)
Win32 Specific Data:
physics
[variable] 109829/4194304 ( 2.6%)
Total Win32 BSP file data space used: 655469 bytes
Linux Specific Data:
physicssurface [variable] 167162/6291456 ( 2.7%)
Total Linux BSP file data space used: 712802 bytes
Total triangle count: 1701
Writing c:\documents and settings\thomas boardman\desktop\mymaps\prefuncdetail.bsp
9 seconds elapsed
** Executing...
** Command: Copy File
** Parameters: "C:\Documents and Settings\Thomas
Boardman\Desktop\mymaps\prefuncdetail.bsp" "C:\Program
Files\Valve\Steam\SteamApps\kerosine99@aol.com\half-life 2
deathmatch\hl2mp\maps\prefuncdetail.bsp"
** Executing...
** Command: "C:\Program
Files\Valve\Steam\SteamApps\kerosine99@aol.com\half-life 2 deathmatch\hl2.exe"
** Parameters: -game "C:\Program
Files\Valve\Steam\SteamApps\kerosine99@aol.com\half-life 2
deathmatch\hl2mp" -console -developer 1 -deathmatch 1 +sv_cheats 1 +map
"prefuncdetail"
The only thing strange is the memorly leak bit, but I don't see how
that would effect the water in game. The problem persists even
after building cubemaps in game and restarting the server.
I have the water surface tied to an env_cubemap that is fairly high
above the water's surface. I also threw a water_lod_control in
for the heck of it. The water itself consists of 2 brushes (since
I didn't want the water brush going through the sloped part of the
pool) all textured with nodraw except the surface.
Here is a shot of it in hammer:
The thing is, I know the texture I'm using is OK, because I have water
in a different area of the map that uses the same texture with no
problems. Although, to be specific I am looking down at the water
in the two in-game shots from a higher point than is possible in the
other area of the map. But I don't see how that would make a
difference.
Does it appear to be going from good to cheap for no reason?