I am having the same problem as described by APShredder in his post in 2009.
The first time I used it, I didn't change the default location, 'My Documents', and it worked fine; but I had to move it to the palettes folder in Paint.Net Users file.
When I tried to use it again for another image it just wouldn't work at all. The UI would flash for a fraction of a second, then nothing -no save- no chance to save.
So, I re-downloaded it. This time the UI came up just like the first time, but I wanted to save in palettes folder within Paint.Net User's File. So I changed the path just as described by ApShredder - clicked ok - and Paint.Net promptly crashed, leaving a pdncrashlog on my desktop. I emailed this as it says to and will also attach it to this post.
Also, about 20 seconds after PDN crashed, my touchpad cursor froze forcing me to do a forced shutdown of my computer. I should probably be saying this somewhere else
(report bugs maybe ?), but this 'cursor freeze' problem occurs frequently when working with the color window.
Edit: After I wrote this post, I restarted PDN and tried the plugin with another image. This time When the UI came up, the offered save location was changed to 'My Documents\Paint.Net User Files\Palettes', and the palette saved ok. So, when I changed the path it crashed the program but it also succeeded in changing the path.
However, when I tried it on another image - (like the first time) - it wouldn't work on a second image. The 'initializing' message would flash and then no UI would appear. What I discovered is that it won't work twice during one session. If I exit then restart
PDN the plugin works again, but only once. It seems this is a one-time-per-session plugin.