This has been reported from time to time.
This can happen also if you lightmap, then paint grass, then alter the terrain by sculpting it.
Go into the matrix panel (Tab Tab) and just nudge one of the grass sliders, It will regen the grass and it will be back on the the terrain again.
Save your map file.
Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz, 2400 Mhz, 4 Core(s), 4 Logical Processor(s), 8gb RAM, Nvidia gtx660, Windows 7 Pro 64bit, Screen resolution 1680 x 1050.