OK, thought long and hard before posting on this thread… 
Seam shadows like that are caused by empty space between the occluder (the wall casting the shadow) and the surface recieving the shadow.
Usually this occurs with patch meshes, but occasionally it can occur with thin or improperly bevelled brushes.
Q3Map2 does some fairly exhaustive testing to figure out the best place to sample light from for each lightmap pixel (luxel). Because there’s just empty space behind the patch meshes, it considers that a valid sample point and it ends up being in shadow.
These types of shadows can be minimized using a number of techniques, such as using -samples N or -super N or -filter on the light commandline. The -samples N switch does “smart” antialiasing, the -super N switch does NxN uniform supersampling, and the -filter switch applies a 3x3 gaussian blur filter to the lightmap data.
You can use -super in concert with -filter for decent results. Using -filter with -samples is more or less pointless, as the filtering blurs any antialiased shadow edges created by the supersampling anyway.
An alternative is to group the patches with the problem shadows into a func_group and add a _lightmapscale key to the func_group with a value of 0.5 or less. Try values 0.5, 0.25, 0.125 and 0.0625.
Cheers,
y