Thanks for your comment.
I rather like the SPI proto area.
But nobody can get things right with their protos, it seems. The real problem with the bad fitting is that your Due is incredibly badly made, as the video amply demonstrates, and it looks like there are problems with the pins on your headers being shorter than normal.
All my standard stuff has 12mm clear between the boards. Your power jack is a standard item and 11mm high, so the proto board should clear it by 1mm. You may rectify the problem by re-installing it properly, and perhaps giving it a lick with a file, but I suspect the header pins are the bigger problem.
The only place I know where you can get decent headers is
http://www.ebay.com.au/itm/Arduino-Stackable-Header-Kit-Extended-Extra-long-15mm-Pins-/130802267649?pt=UK_BOI_Electrical_Components_Supplies_ET&hash=item1e746c3601
These are actually used for clearing an Ethernet socket and should not be necessary for a competently-made board. You may find that standard headers will suffice, if yours are shorter. The standard pin length is 11mm.
The other board, ARD-0046, seems to be a better bet, and will be my next proto board. If I had known before what I know now, I would have had one of those already. It is half the price of the Freetronics.
Thanks.