Hi Sam,
There are three ways of getting rid of the squares;
You can reduce the gamma parameter until you can't see them anymore
You can increase the 'Sample Size' in the setup screen to something larger.
You can increase the 'Image Diameter' to something larger.
What you're seeing is the result of Synth 'running out of starlight to scatter'. For very bright stars, a large amount of light needs to be diffracted/scattered. Same thing for 'close ups' (that's why image diameter makes a difference as well). If the amount of light to scatter/diffract doesn't taper off quick enough (because a star is very bright and your gamma adjust doesn't help) then you'll see a boundary where Synth ran out of puff. You can enlarge that area (and extend the boundary) by using a higher Sample Size.
It's a trade off I had to make to make things act physically correct, yet only apply to the stars so it doesn't wash out anything else.
Looking at your StarTools screenshot, it seems your Image diameter is off quite a bit for a big object like the Orion Nebula. You'll find you'll get better (and more life like!) results if you try to approximate your gear's aperture, focal length and the diameter of the image in arc minutes. Then finish it off with setting your gamma a bit lower and (depending on seeing conditions in the rest of the image) add a tiny bit of blur.
Let me know if that helps!
PS There's a StarTools forum as well