NOTE: This issue should now be completely fixed by an update done to Spot. Please be sure you are running the latest version.

If you encounter the situation where you have created a DS9 regions file and try to use this overlay in Spot/Leopard, and no region gets overlaid on the image that you have loaded/retrieved in Spot/Leopard, the reason is that the overlay tool expects the regions file to be of v3.0. Unfortunately, the most recent version of DS9 is v4.1. The format of the regions file in v4.1 is different than v3.0 in the following way (by example):

region definitions in DS9 version 3.0 looked like
fk5;circle(123.4, 60.2, 10")

But in DS9 version 4.1 they changed the semicolon to a newline:
fk5
circle(123.4, 60.2,10")

We have updated this within Spot, but have not yet auto-updated to invoke this change (as of 2012 Oct 12).

So, the workaround, for now, is to modify the regions file, to join the two lines, with a semicolon between the coordinate system and the region type, and it will work in Spot.