It is possible that you have tried to code off the edges of the block diagram. The block diagram location is a 16-bit integer, so has limits of -32768 to +32767. If you try to put code outside these limits, weird things happen. But that's not all. There are some roundoff bugs which may cause insanities if you try to connect objects farther apart than about 15,000 pixels. To be safe, you need to limit your code to within about +/-7500 pixels of the center of the diagram.
Note that you should use subVIs and never create a VI with a block diagram greater than a couple of screen widths wide, anyway. Anything else is too difficult to maintain or debug.
