I've seen this to. It seems that once you restart the CK, the Grid gets reset to an arbitrary orientation.
I stopped dealing with it, and started working off grid for everything. Takes longer in the beginning, but it starts going quicker after a bit of work.
Also, wouldn't it be nice, if we could snap larger objects back to grid? Select 14 floor pieces not on grid, click them, snap them back to grid. Would make life so much easier.