If I restart my game, then it is fine for a little bit, however, it will come back again eventually. Sometimes setting a 'mark' in that area, then walking off, and using the 'mark' to get back also makes me fall through the ground in that area.
Is it always the same location?
About the goto and mark commands: They we're not officially working yet, so they may cause you fall through the ground often. It is only strange when collision never loads for an area, i.e. returning to surface by using F2 and still falling through ground.