Try copying and pasting your map into a new file. The lighting bug is not fixable without doing that, but the shadows are an issue with excessive stretching of displacements which warp the lightmaps. Do they happen in every version you compile?
It's weird because i first saw this after Valve broke the SDK or the compilation executables or what ever. After the supposed fix most people stopped seeing this kind of thing but it does look exactly like the symptons from that original borked SDK update. Personally i havn't run into this, did replacing the geometry into a new vmf file work?